So, I have put this thing together, for the other BFG;A2 players in the crowd and anyone else interested. Please note that this was not created with balance in mind, which is why I have not included any fleet point costs per ship.

Battlefleet Gothic Armada 2: The Protectorate United Navies; part 1

Faction-wide ship attributes:

Disciplined:
+25 Bravery.

Good Troop Efficiency:
2 Troop damage per assault action.

Planned Strike:
30% chance to deal 1 additional Troop damage per assault action.

Panacea:
15% chance to reduce Troop damage from enemy assault actions by 1.
decreases the chance of collateral troop damage by 20%.

For Cain!:
Replaces Encouraging Speech with the By Cain's Will! Command Skill: Replenishes morale by 600 and grants double critical chance for all weapons and skills for 30 seconds.

Plasma Reactor:
Grants access to the All Ahead Full, High Energy Turn and Burn Retros maneuver skills.

Gravity Engine Assisted Thrusters:
Reduces the combustion point cost of maneuver skills by 50%.
+80 Speed for Light cruisers and Cruisers.
+40 Speed for Battlecruisers and Grand Cruisers.
+50% Rotation Speed for all ships.

Advanced Close-In Defense Systems:
+50% Defense Turret range.
+10% Defense Turret accuracy.

Phased Void Shields:
The Shield bar is divided into 5 sections. Each section recharges independently. Multiple shield sections recharge simultaneously.

Heavily Automated:
Decreases the chance of suffering critical damage by 20%.
Negates the impact of depleted crew steps.

Borg Sensors:
+4500 Identification Range.
All enemy ships within half range of the ship's Identification Range are marked and revealed for 45 seconds.

Protectorate Navy Strikecraft Squadrons:

Cain Wing Interceptor Squadron:
Behavior: Can be sent to target/protect a ship or any point on the battlespace. Opens fire on enemy squadrons and torpedoes while moving. Patrols for 90 seconds, targeting enemy squadrons and turrets. Skill charge is recovered upon return to its carrier.
Aircraft per Squadron: 6
Speed: 650 units per second
Dodge: 80%
Toughness: 2

Cain Wing Fighter Bomber Squadron:
Behavior: Targets enemy ships only. Opens fire on enemy squadrons and torpedoes while moving. Once their bombing run has been performed, the fighter bombers gain +20% dodge change and behave like an interceptor squadron. Skill charge is recovered upon return to its carrier.
Aircraft per Squadron: 6
Speed: 650 units per second
Dodge: 60%
Toughness: 2
Hull Damage: 30
Critical chance: 25%
Armor Pierce: -25 target armor

Black Hawk Assault Transport Squadron:
Behavior: Targets enemy ships only, performs 1 assault action per transport. Opens fire on enemy squadrons and torpedoes while moving. The escort fighters protect the assault transports and once the transports have performed their assault action they turn into an interceptor squadron.
Aircraft per Squadron: 2 + 4 escort fighters
Speed: 650 units per second
Dodge: 60%
Toughness: 3
Troop Damage: 2
Critical assault chance: 30%

Protectorate Navy Weapons:

Macro Cannon:
Damage: 21
Reload time: 12s
Range: 13500
Critical chances: 5,25%
Accuracy: 80%/60%/40%/20%/0%

Heavy Macro Cannon:
Damage: 21
Reload time: 12s
Range: 18000
Critical chances: 5,25%
Accuracy: 80%/60%/40%/20%/0%

Light Lance:
Damage: 15
Reload time: 12s
Range: 9000
Critical chances: 7,5%
Accuracy: 100%
Armour Pierce: -25 target armor

Lance:
Damage: 15
Reload time: 12s
Range: 13500
Critical chances: 7,5%
Accuracy: 100%
Armour Pierce: -25 target armor

Heavy Lance:
Damage: 15
Reload time: 12s
Range: 18000
Critical chances: 7,5%
Accuracy: 100%
Armour Pierce: -25 target armor

Superheavy Long Pattern Lance:
Damage: 45
Reload time: 12s
Range: 22500
Critical chances: 15%
Accuracy: 100%
Armour Pierce: -35 target armor

Grand Slam Nova Cannon:
Reload time: 50 seconds
Range: 6000-30000
Accuracy: 100%

Grand Slam II Nova Cannon:
Reload time: 30 seconds
Range: 6000-30000
Accuracy: 100%

Protectorate Navy Ammunition:

Nova Cannon Plasma Warhead:
Area of Effect: 2000
Damage: 400-200 from the center to the edge
Armor Pierce: -100 target armor
Morale damage: 100

Nova Cannon Void-Collapse Fusion Warhead:
Area of Effect: 3000
Damage: 600-300 from the center to the edge
Armor Pierce: -100 target armor
Morale damage: 150

Nova Cannon Graviton Warhead:
Area of Effect: 3000
Damage: 20 per second
Armor Pierce: -100 target armor
Duration: 30 seconds
Slows ships down by 75% and pulls them towards the center of the Area of effect.

No.9 High Yield Homing Torpedoes:
Damage: 100
Armour Pierce: -25 target armor
Critical chances: 25%
Target Tracking: 2,5° per second
Arming Distance: 1000
Ignores Shields/Holofields

No.5 E-WAR Candela Torpedoes:
Reduces weapon accuracy by 20% for 20 seconds per hit.
Deals 30 Morale damage per hit.
Forces a random skill set on 50% cooldown per hit.
Destroys 2 turrets per hit.
Target Tracking: 2,5° per second
Arming Distance: 1000
Ignores Shields/Holofields

Light Cruisers:

Protector Class Light Cruiser:

Shield: 240
Hull: 1200
Defense Turrets: 12

Front Armour: 67
Side Armour: 67
Rear Armour: 67

Identification Range: 13500

Speed: 240
Rotation Speed: 18
Boarding damage: 4
Lightning strike damage: 2
Critical Assault chance: 30%

Bravery: 25
Troops number: 11

Weapons:
2x Light Lance Turret - 1 Attack, 270° Front
2x Launch Bay

Attributes:
X-35 Void Shield - +20% Shield points

Assault Skills:
Boarding Action - 2 charges; 2 Assault actions
Lightning Strike - 2 charges; 1 Assault action
Transfer Troops

Weapon Skills:
Cain Wing Interceptors - 2 charges
Cain Wing Fighter Bombers - 2 charges
Black Hawk Assault Transports - 2 charges

Maneuver Skills:
All Ahead Full
High Energy Turn
Burn Retros

Stance Skills:
Brace for Impact
Running Silent
Lock On
Reload

Command Skills:
Scanner
Canticle of the Omnissiah
Call to Arms
By Cain's Will!

Courageous Class Vanguard Cruiser:

Shield: 240
Hull: 1200
Defense Turrets: 12

Front Armour: 83
Side Armour: 67
Rear Armour: 67

Identification Range: 13500

Speed: 280
Rotation Speed: 18
Boarding damage: 4
Lightning strike damage: 2
Critical Assault chance: 30%

Bravery: 25
Troops number: 11

Weapons:
4x Prow Torpedo Tube
2x Triple Macro Cannon Turret - 3 Attacks, 270° Front
1x Twin Lance Turret - 2 Attacks, 270° Front
2x Launch Bay

Attributes:
X-35 Void Shield - +20% Shield points

Assault Skills:
Boarding Action - 2 charges; 2 Assault actions
Lightning Strike - 2 charges; 1 Assault action
Transfer Troops

Weapon Skills:
No.9 Homing Torpedoes - 2 charges
No.5 Candela Torpedoes - 2 charges
Cain Wing Interceptors - 2 charges
Cain Wing Fighter Bombers - 2 charges
Black Hawk Assault Transports - 2 charges

Maneuver Skills:
All Ahead Full
High Energy Turn
Burn Retros

Stance Skills:
Brace for Impact
Running Silent
Lock On
Reload

Command Skills:
Scanner
Canticle of the Omnissiah
Call to Arms
By Cain's Will!

Furious Class Light Cruiser:

Shield: 240
Hull: 1200
Defense Turrets: 12

Front Armour: 83
Side Armour: 67
Rear Armour: 67

Identification Range: 13500

Speed: 280
Rotation Speed: 18
Boarding damage: 4
Lightning strike damage: 2
Critical Assault chance: 30%

Bravery: 25
Troops number: 11

Weapons:
1x Prow Mounted Superheavy Long Pattern Lance - 1 Attack, 90° Front
2x Triple Macro Cannon Turret - 3 Attacks, 270° Front
2x Broadside Torpedo Silo

Attributes:
X-35 Void Shield - +20% Shield points
Broadside Torpedo Silos - tripled charges for all Torpedo weapon skills.
66% reduced reload time. 2/3/3/4 Torpedoes per salvo per silo for Light Cruisers, Cruisers, Battle Cruisers and Grand Cruisers.

Assault Skills:
Boarding Action - 2 charges; 2 Assault actions
Lightning Strike - 2 charges; 1 Assault action
Transfer Troops

Weapon Skills:
No.9 Homing Torpedoes - 6 charges
No.5 Candela Torpedoes - 6 charges

Maneuver Skills:
All Ahead Full
High Energy Turn
Burn Retros

Stance Skills:
Brace for Impact
Running Silent
Lock On
Reload

Command Skills:
Scanner
Canticle of the Omnissiah
Call to Arms
By Cain's Will!

Investigator Class Light Defense Cruiser:

Shield: 240
Hull: 1200
Defense Turrets: 12

Front Armour: 67
Side Armour: 67
Rear Armour: 67

Identification Range: 18000

Speed: 240
Rotation Speed: 18
Boarding damage: 4
Lightning strike damage: 2
Critical Assault chance: 30%

Bravery: 25
Troops number: 9

Weapons:
2x Light Lance Turret - 1 Attack, 270° Front

Attributes:
X-35 Void Shield - +20% Shield points
Argus Sensor Array - +4500 Identification range. +2000 Scanner Command skill range. Passively triggers the Scanner Command Skill every 30 seconds.
Vigil Laser Defense Array - The ship has 10 additional defense turrets, these turrets have a range of 9000.
Prognosticarium - Fleet buff: +5% accuracy for ships firing at marked enemies. Improves Target Tracking for Torpedoes against marked enemies by +1° per second.

Assault Skills:
Boarding Action - 2 charges; 2 Assault actions
Lightning Strike - 2 charges; 1 Assault action
Transfer Troops

Maneuver Skills:
All Ahead Full
High Energy Turn
Burn Retros

Stance Skills:
Brace for Impact
Running Silent
Lock On
Reload

Command Skills:
Scanner
Canticle of the Omnissiah
Call to Arms
By Cain's Will!