The details of this Universe:

Autobot and Cybertron Leaders

Prima –- "May Primus light the path to your destiny."
First Guardian of the Matrix, now long dead. His teachings helped to advance Cybertron society, and sparked the pursuit of knowledge within the Transformer race. He is considered both a legend and a myth by modern-day Cybertrons. It is said that he had a direct link to Primus himself.

Prime Nova -- "The only true freedom is the freedom to be ourselves."
Prima's first successor. He is a dedicated explorer, intent on finding new life, and to extend peace and alliance throughout the galaxy. It is he who gives Cybertron its interest in other planet's affairs.

(A long gap, many leaders for many millions of years, until we get these guys- the leaders during the war:)

Imperatrix Prime -- "What rises must fall, but what has fallen will rise again."
The first Matrix-keeper during the war, effectively appointed leader of the Autobot movement. Her role against the Decepticons became pivotal in the burgeoning conflict, as she was responsible for moulding the Autobots into a fully-fledged, organised force. Prior to her adopting the mantle of leadership, Cybertrons who defied Decepticon rule were simply detained as POW's or executed outright, her efforts lead to the liberation of many captives. She regularly received criticism for "poor decisions" purely on the basis that she was female. Despite this, she was able to let the Autobots get a foothold in the war, especially after the acquisition of the Decepticons transforming technology.

Tector Prime -- "Defence through vigilance."
Under his command, the Autobots were able to drive off the Decepticons and regain a large number of the ruined city-states, which were promptly converted into effective underground bases (to make them still appear deserted). He established AutoBase, amongst the wreckage of Iacon, as the primary command centre and instituted commando groups such as the Wreckers and the Lightning Strike Coalition. He also called for a massive assembly programme to try and boost the number of Autobot troops, so as to defend their new territory.

Amicus Prime -- "True strength lies in friendship."
Another female Prime. Her origins were originally that of Neutralist, making her an oddity amongst Matrix-keepers. She continued what Tector Prime started; driving the Decepticons back and maintaining their ground. She was also successful in absorbing the remaining Neutralists into the Autobot ranks (providing a significant number boost) and gained access to what Sub-groups had not defected to the Decepticons, this included Omega Supreme.

Calcifax Prime – "I fight for justice, and I plan on winning."
A courageous warrior, he led many assaults against the Decepticons. He preferred to lead by deed rather than word, and do his part in the field with his weapons array rather than from behind a desk at AutoBase. He felt that the Autobots needed to use more ingenuity in their basic war methods, and decreed that they should develop new devices of their own accord rather than simply backwards-engineering Decepticon technology as it developed, this attitude leads to many concepts but most notably the Targetmaster concept.(1) He even clashed head-on with Megatron at the smelting pools of Tyrian, where he famously dragged the Decepticon leader into a (supposed) molten grave at the cost of his own life.

Sentinel Prime -- "Freedom is the right of all innocent beings."
Vastly different to his predecessor, he believed in a silent, carefully planned victory as opposed to straight-out warfare. With the Decepticons now lacking a stable hierarchy, the new Sentinel Prime utilised sabotage to hinder their recovery even further. He was able to bring a number of other city-states under Autobot control, and even acquired Space-Bridges that double agents could use to usurp other planets of Decepticon control. Unfortunately, his destabilisation of the Decepticon army was only partially completed when Megatron returned…

Optimus Prime -- "Freedom is the right of all sentient beings."
Do I truly need to tell you about this guy?

Novus Prime -- "Experience is the benchmark of maturity."
(Quintessentially a re-named Rodimus Prime. Because his name sucks.)

Recepticon and Military Leaders:

Megatron -- "Peace through tyranny"
Megatron was the supreme allied commander of the Cybertronian military, supposedly being a descendent of the Liege Maximo. (Allegedly one of the original thirteen, and the founder of the military.) Even before the war broke out, however, Megatron had dark intentions. Intending to use his 'Deception' forces to eventually usurp the high council and perform any number of military oriented plans, Megatron gleefully realised that the war allowed him to place Cybertron under martial law with good reason. Note that Megatron's 'Deception' forces, being his closest legions, may have contributed to the name 'Decepticon'.

Shockwave -- "Clarity of thought before rashness of action."
Cold, calculating and thoroughly logical, so owning one of the Microsoft of the Transformers world is a no-brainer. He detests having Megatron, someone who he considers to be all brawn and irrational being in control of the merged factions.

Starscream -- "Conquest is made of the ashes of one's enemies."
Chief scientist for both Recepticon and Military forces alike, Starscream was in-charge of many of the more twisted Decepticon ideas, including the pulping of living tissue for batteries in the early powermaster process. Believing that his pioneering efforts gave him a right to move to higher places, he constantly attempted to gain the role of chief aerospace commander. Megatron eventually fell-through, assuming that this would appease his power-lusting nature.

Sub-Groups:

Headmasters: When the conflict against Optimus Prime showed no sign of diminishing, even by Transformers standards, Shockwave decided to restart the "Infiltration" program of the original Recepticon Corporation in hopes of rejuvenating their dwindled resources. Hundreds of Decepticon teams were dispatched into the galaxy, ordered to follow Infiltration protocol to the letter and incorporate as many worlds as possible. The Autobots, realising the extremity of the situation, responded in kind and set off to stop them. However, it quickly became apparent that the native inhabitants of these worlds did not take kindly to giant robots "invading", and the Autobots were forced to fight a secret war against their foes.

One such planet to be selected for Infiltration was the relatively small world of Nebulos. Long ago, before the outbreak of war, this planet had been next in line for colonisation and enslavement, but was never approached. Still finding it and ideal material source even after all this time, the Decepticons arrived under the command of the titanic Scorponok. Fortress Maximus and his team arrived several months later to find the planet was already gripped in a one-sided conflict, with the Nebulons taking heavy casualties.

Realising that standard procedure would not work, Fortress went straight to the Nebulons themselves and offered to help them drive off the invaders. The Nebulons remained hostile, not believing Fortress' claims of two armies. As a display of his sincerity to help them, Fortress Maximus stated that he would surrender his body for Nebulon analysis and dismantling, so long as they did not tamper with his spark (1). Many of the Nebulons were still sceptical, until Chromedome, Hardhead, Brainstorm and Highbrow also offered to undergo the same procedure. The examination of their robotic bodies and weaponry allowed the Nebulon rebels to backwards-engineer many Cybertronian weapons systems and upgrade the armour plating on their crafts. Whilst Brainstorm and co. remained mostly intact, Fortress was almost entirely dismantled.

Despite their best efforts, the Nebulons were still fighting a losing battle; they required heavy artillery. Fast. Thus it was decided to re-activate the stasis locked Autobots. This decision did not bode well with all of the Nebulon leaders, who felt that it would be disastrous if the Autobots betrayed or abandoned them. Subesequently the Autobot's heads were dismantled and redesigned into protective suits for chosen Nebulon soldiers, but were incorporated with transformation mechanisms that allowed them to reassume the form of a robot head at will.

In theory, this effectively let them pilot the larger forms unhindered. However, the process was rushed and imperfect, as a result the procedure created two fused minds as opposed to simply a Nebulon soldier in a robot body. Neither party was truly happy with the outcome, but persevered. Fortress Maximus was all but completely rebuilt, with a notably larger body, so much so that a mid-way drone (dubbed "Cerebros") was required to allow Galen to merge with Fortress.

Through their double agents at Nebulon HQ, the Decepticons caught wind of the project and emulated it (assuming that it somehow made the resulting Transformer all the more powerful) before the Nebulons discovered that the process didn't work. Needless to say, they were somewhat disgusted with the end result, but fought on against the Autobots regardless.

Targetmasters: One of the many results of Calcifax Prime's decree of innovation as well as the very first "Master" process. Targetmasters are the product of attempting to create the ultimate warrior, in terms of both firepower and precision. Firstly, expert marksmen were selected to oversee the construction of the project in hopes of maximizing the efficiency of the weapons. The result was quite promising; a compact firearm that contained almost a dozen particle-accelerators, making them ludicrously potent.

The next step was the addition of a superstructure, along with basic circuitry, this allowed the weapons to transform into semi-sentient robots and act as recon scouts for their larger counterparts when not in combat. Finally, the marksmen themselves underwent a procedure that allowed the Target-bots to connect with their forearms and act as weaponry; the experienced mind of the marksmen handled the aiming, whilst their partners were responsible for the degree of firepower used on a target.

However, something rather unexpected happened, once both beings had undergone this operation, their minds became psychically linked. This became a very desirable side effect, as it enabled better performance in the field. The process fell into Decepticon hands when three of the marksmen turned traitor, in exchange for pardoning and recruitment into the Decepticon army (2).

Much later, the process was expanded upon and was dubbed "Project: Double Target", this allowed for the larger Transformers to utilise two Target-bots at a time as opposed to just one. This method is considered somewhat unorthodox, as the larger robots are unable to use their hands when combined with both of their partners.

Powermasters: Millenia ago, when Recepticon Corp. was one of the largest companies in the expanding galactic trade, R-Corp researchers began searching into a method of utilising organics as an optional power source. Those chosen were regressed into a vegetative state, and stored in tube-like containers for use by Transformers in the field.

The experiment was abandoned, since the 'batteries' were too large to be carried or used as part of an emergency pack. The conversion was also not very cost-effective, as the organics had to be constantly maintained (E.g.: heat, nutrition, waste disposal etc.) to ensure an optimum energy output, which itself was still minimal.Upon discovery of this technology, the Autobots snapped it up but were unable to utilise it for a remarkable amount of time. When Fortress Maximus requested reinforcements for his Nebulos party, the designs were heavily modified and put into operation alongside the Headmaster process. The modifications ensured that those selected for the process were not reduced to a vegetative state, but instead they were cybernetically augmented with Cybertronian technology, allowing for a far larger energy output. The primary reason for the procedure was to strengthen their alliance with the Nebulons.

The Decepticons emulated the procedure for similar ends, forming ties with Nebulons who shared their vision of conquest.

Omega Sentinels: Due to the escalating political tensions between the Neutralists and the burgeoning Decepticons, scientists were searching for new options in terms of mass peacekeeping. Thus, they referred back to the defunct "Sentinel" models and began research on the 'Gamma' and 'Omega' models respectively. After much deliberation, Omega Sentinels were put into manufacture, whilst their Gamma counterparts were not deemed cost-effective (due to excessive fuel consumption) and the singular prototype was placed into storage (3).

Omega Sentinels were used primarily to protect Neutralist establishments that came under attack from Decepticons, and they proved remarkably effective. However, as the war dragged on, Omega Sentinels fell into disrepair due to the Neutralists not having the resources to maintain then. Eventually, the Neutralists took up arms and sided with the Autobots, taking their remaining Sentinels with them. Once repaired, heavily upgraded and granted the gift of a spark, resulting in the birth of Omega Supreme.

Gestalts: In an ironic twist of fate, one of the most destructive technological achievements in the Cybertronian war is a Neutralist concept. Gestalt technology was created as a response to the arms race between the Autobots and Decepticons. Neutralists, fearing for their own safety, designed a process that allowed members of their number to merge together and form a powerful defensive force. This technology kept them safe for many decades, till it forcefully fell into Decepticon hands. When the Neutralists sided up with the Autobots, the technology was handed over to them as an offer of gratitude, allowing the 'Bots to strike back with their own combined titans.

Note that many sub-groups are literally 'special teams' or specialised forces. These were derived in a similar way to human special forces: IE- The Naughticons are adapted for a naughtical environment. (Naughticons are renamed Seacons, as the name is crap.)Pretenders: The ultimate form of Infiltration protocol, Pretenders are created by moulding an outer shell around a Transformer. The Transformer is still conscious were inside the shell, and can emerge whenever they like, the shell then reforms and fights alongside their possessor (some shells also have the ability to transform). The shells are constructed from "Synthoplasm", a synthetic organic substitute that is malleable in its early stages. This allows it to be moulded into any shape or form; ideal for replicating the appearance of a species and infiltrating their society unnoticed (4). The Pretenders' manifestation is often modelled on the likes of important figureheads (E.g.: politicians) or simply an original generic template (allowing them to look like a member of the public). If the former is chosen for an outward appearance, then the original being is dispatched and replaced with a Pretender double.

Pretenders can either choose to remain with their shell whilst on an operation, or separate and tend to matters elsewhere, leaving the shells with an automated task, this factor makes the Pretender agents twice as effective. Autobots also use Pretender technology as they find it prevents them from drawing unnecessary attention to themselves, yet it still remains a primarily Decepticon technology due to the Decepticons being able to create Synthoplasm far more efficiently.

Transformers who have become Pretenders often keep their shells after a mission has concluded, and a planet usurped. This tends to make them stand out when removed of their initial environment.

Micromasters: Simply put, these diminutive Transformers are used as spies. They came about because breakthroughs in scanning technology meant that Transformers could be detected through an "energy signature", regardless of how well they hid themselves. Thus, a large number of Autobots were "downsized" and used for espionage and reconnaissance, as their small size prevented them from being noticed on scanners (primarily because their tiny energy signatures are overlooked as either maintenance droids, or simply glitches on the screen). Decepticons later mimicked the procedure. Micromasters are looked down upon by most of their peers, figuratively and literally. Decepticons, however, go to the extremity of viewing them as vermin that deserved to be stepped on. This global abhor often means that Micromasters on both sides share a strong bond of camaraderie, and are rumoured to have drinking matches with members of the opposing army.

This was later to become espionage technology in the form of cassettes, when they were made slightly larger so as to be more effective combatants.

Duocons: The earliest documented approach to a Triple-changer concept; once the breakthrough had been accomplished, Duocons were rendered obsolete. However, the finalised beings themselves (or rather those who managed to stay sane) are still active and fighting in the war.

Clones: Responding to Tector Prime's demand for as many troops as possible, Autobot scientists attempted to clone some of their existing warriors as opposed to building more from scratch. This meant that they could save on both raw materials and time-management for building a new body. The process split a spark at a base level and produced an exact copy from the splintered segment. Whilst initial batches were a success, Cloned transformers often had a distressingly short life span (due to the nature of their sparks) and could suffer from serious mental complications as they rapidly matured. As such, the process is no longer attempted en masse.

Aquaspeeders: One of the many results of Calcifax Prime's decree of innovation. These Autobots were outfitted with new weapon tech; highly efficient molecular acid rifles. The weapons fired a powerful stream of acid at a target, melting it into molten slag in a matter of minutes. So as not to damage themselves, the 'Aquaspeeders' were submerged in a chemical bath that impeded the effects of the acid on their bodies. Currently Aquaspeeders remain an Autobot-only splinter group, as Decepticons find the acidic compound rather hazardous to store and have been unable to acquire the immunity chemical to aid their own troops.

Sparkabots/Infernocons: Autobots researchers attempted to re-engineer Energon, but instead were able to concoct a new propulsion system. Whilst Energon itself is 100 energy efficient, if they are unable to use it, they have to use whatever they can find.

Thus they develop a substance is that 'dismantles' atoms, ripping them of their electrons and the atomic energy they contain, regardless of them being radioactive or not, converting them into carbon (hence the likeness to flames). The finalised process is somewhat simple; fuel is inserted, gets converted into as much energy as possible and gets pushed out the other end. This substance was named Perussix: A perfect propulsion system. Clean, fast and requires the minimum amount of parts, all that is needed is a canister of the substance, a tube and some form of end to allow the thrust to leave.

However, there is one flaw in this method: it doesn't work.

The 'Atomic fire' burns everything on a molecular level. It cannot be smothered and simply carries on 'dismantling' until it runs out of fuel. Then it stops. The three volunteer Sparkabots were fitted with this propulsion system, only to realise that they had to keep on consuming matter so that they were not burnt to a crisp from the inside out. For example, if someone got some of this substance on their hand, they wouldn't be able to stop it. Their choice is to either die a slow and painful death, or cut off their hand. Stopping it wasn't an option. For obvious reasons, this technology was dropped.

The Decepticons eventually acquired the technology and found it quite intriguing, if a tad promising. The process was quickly converted into use for weaponry, specifically; Flamethrowers. Unfortunately, said flamethrowers had to be constantly 'fed' matter to prevent them from melting both themselves and the Infernocon test-subjects they inhabit. Regardless, the Decepticons sent them into the war zone anyway, where they proved to be equally devastating to their own forces as the enemy's.

Turbomasters: After the relative success of the Infernocons in battle, Decepticon scientists sought to rectify their inherent instability. By this point in the war, the Infernocons themselves had become a truly lost cause in terms of both mental and physical health, so much so that Flamefeather reverted to a catatonic state. This allowed for a fairly easy capture of all three renegades. Extensive testing caused the Infernocons to finally meet their overdue, painful end, but their demise was not without incentive. Utilising magnetic-field generation technology, scientists were able to isolate the Perussix substance and began to backwards engineer its properties. Deciding that its corrosive properties had no real practical use, they experimented by binding the Perussix particles to photons, effectively creating "corrosive light"- a substance that could burn and cut through anything, to a degree, in the guise of a laser beam. The magnetic generators themselves then underwent a downsizing, remoulding them into hand-held, though somewhat bulky, weapons for use in the field.

However, the Decepticons were unable to put this mechanism into use, as the plans, reports and research logs were all stolen; this included the husks of the Infernocons. The culprits in question were the Turbomasters, who had gotten wind of the operation and chose to ransack it, despite lacking orders to do so. Upon acquisition of the weaponry, Thunderclash was ordered to seal them away permanently. Instead, Thunderclash chose to research further still into the systems, and was able to conclude that they would make suitable secondary engines for an automobile transformer. This, combined with their current frame modifications, allows the Turbomasters to achieve insane speeds when taking to the roads.

(1) That's right folks, no head-rippage here! It's all good, clean alien autopsies.
(2) This was mainly inspired by Pointblank/Blanker's line in Headmasters, when the Cybertrons discovered that three of the Master refugees had defected to the Destrons, those who had allied with the Cybertrons became distressed at the loss of their friends. Pointblank consoled them by stating "We know how you feel…" followed by a glare at Slugslinger, who open-fired.
(3) Rumours that the Gamma prototype was stolen have been explicitly denied.
(4) Bludgeon was originally intended to be modelled on a Japanese human, but a malfunction in the moulding process resulted in the face not being formed properly. He kept his shell in the end, finding it made him more intimidating.