I'll cut to the chase, this story isn't going to get updated. But I'll post what would have happened.
Premise: Aero is a pokemon human hybrid, he can transform into any pokemon, and transform into a human. He is the result of a mix of Human and Mew DNA. He escapes out of the lab he was held in and goes on a pokemon journey to become strong enough to take down Team Rocket.
Aero: is smart and clever, but really emotionally stunted. He looks out for himself and those he cares about first. But that changes over time as he connects more with the world. He was traumatized but he works through the trauma to become stronger. He goes around seeking new ways to become stronger to achieve his goal. To take down Team Rocket. He is also incredibly emotionally stunted and really doesn't know how to talk to people, despite his desperate wish to be accepted. This conflict between his secret desires of social acceptance and his trauma creates in effect the strong silent type with a heart of Gold. He also develops a strong sense of justice and actively looks to prevent what happened to him. In short, as he becomes stronger he develops from True Neutral to more of a neutral good.
What happens: Born in a lab, Aero was initially experimented on but was taken in by Mr. Fuji along with Splice (Mewtwo), due to a mix of circumstances, among them Mr. Fuji being a decent human being. Aero ends back up in the lab against his will around the age of 10. He then breaks out of the lab along with Mewtwo and ends up in Waterfall town. A medium town located in Johto in the far west. He spends a couple of years here but was ostracised by his peers. Eventually, Team Rocket finds him and Splice and ends up burning the town to the ground. They capture Splice and Aero, but Team Rocket's actions attract the attention of the G-Men along with the Pokemon Leauge.
Despite this attention, the experiments continue and under worse and worse conditions. After being pushed far past their limits Aero and Splice break out once again but are separated. At this point, Aero meets up Kip (Mudkip) Arianna (Ralts) and Arun (Riolu) band together and end up sneaking through Johto and Kanto. Team Rocket's presence in Kanto has been heavily reduced thanks to Red Ketchum They end up at Lavender town where Aero meets back up with Splice and Mr. Fuji. At this point, Aero tries and lives somewhat of a normal life. Team Rocket is "disbanded" or at least goes underground once again for a time.
At some point though, Mr. Fuji and Aero begin hearing rumors of Rocket activity. This causes Aero to start on his pokemon journey in an attempt to become strong enough to take on Team Rocket. At this point, Steven goes around and starts collecting badges for the Indigo Plateau Conference. He places 16th-10th in the Leauge due to his small team size, among other things. After this and some sort of Rocket activity, Aero has the confidence to set out on his own.
Aero then goes to Johto and while collecting badges Visits Waterfall town. He vows to avenge the residents of the town and any injustice he comes upon. There are a few more encounters with Team Rocket, but at this point, Giovanni's goal is to stay undercover. He places in the top 4th in the Silver Conference.
At this point, Ash starts his pokemon Journey.
Aero at this point has grown to love pokemon battles and hears to the Hoenn league and decides to try it out. Exploring through Hoenn captures a couple of pokemon and ends up winning the Ever Grande Conference. This is his first Pokemon league challenge and he beats Syndey and comes close to beating Phoebe. After recovering from the defeat, he gets a call from Mr. Fuji about increased Rocket activity. This leads to the Aero coming back to Kanto to investigate the claims. During this search, the events from the first pokemon movie occur really without any intervention from Aero. He only shows up at the end investigating the strange weather surrounding the island. He and Splice talk to Mewtwo (to both their shock) and end up getting a lead on Team Rocket. This leads to a showdown with Giovanni, but he escapes.
While Ash is in the orange islands, Aero is continuing to train and begins meeting with the legendary pokemon of the region. He begins capturing and releasing them. And then burying the Pokeball. It is at this point that Steven attracts the attention of the G-Men and the international police. Aero expresses his interest in joining but doesn't at the time. He later captures Moltres Articuno and Zaptos after the events of the second pokemon movie.
While Ash heads off to Johto, Aero proceeds to head to Sinnoh and wins the Lilly of the Valley conference. He then beats all of the Elite Four but looses to Cynthia. He keeps in touch with the international police and the G-Men and hears about a trainer called Ash Ketchum, and his various exploits across Kanto, Johto and the orange islands. Aero decides to travel and investigate new rumors of two criminal teams called Team Aqua and Team Magma in the Hoenn region. One of his first stops in the region is the city of Alto Mare. Aero ends up playing a great roll in this movie. Investigating rumors of legendary pokemon, he is initially at odds with Ash and crew. However, Aero ends up earning their trust along with Latios and Latias, and captures them and then releases them. However, Annie and Oakley still steal the Soul Dew and send the city into lockdown. Aero's intervention though lessens the time Latios is spent captured. However, the tsunami still comes into the city. But Aero and Splice partner up to use their powers to save the city. It is at this point revealed to Ash and crew what Aero is. Aero ends the movie by waving to Ash and telling him, they will meet up again, before teleporting away holding Annie and Oakly to turn them into the international police.
Aero then investigates rumors of Legendary Pokemon and goes around capturing rare and legendary pokemon. He also investigates both teams and records what they do. He is unable to keep cover when dealing with any kind of experimentation, however. He also spends some time in Unova slowly grabbing Gym badges when he has the time. Hearing about an old Team Magma member Bulter Aero decides to see why he left. This leads to the events of the 6th pokemon movie. Aero participates in the festival and asks Butler why he left. After seeing his desire for revenge Aero asked for any information that could be used against Team Magma. And they form a working relationship for a time. Aero after saying hello to Ash and giving him his pokenav number leaves. The events of the rest of the movie play out until Groudon comes to life. Aero responds and is able to beat back Groudon with the help of Ash and Butler. Due to Aero's intervention along with Splice and stealing Ashes of the Past's solution. Max gets to continue to spend time with Jirachi. Aero also parts on good terms with Butler and Diane.
At this point, Aero decides to go to Unova and participates in the Unova pokemon league conference at Ventress City. He then goes on to beat Alder, but gives the championship back to Alder, stating that he wanted the battle. After this success Aero becomes an official agent for the international police. Note Steven usually shows up after the events of the pokemon movie to capture whatever legendary pokemon are featured.
Whether if Aero participates in the movies I don't mention is up in the air. I'm not going to write him in every single major event unless he has a good reason to be there.
Eventually, the clash between Groudon and Kyogre happens and Aero is center stage. He plays a key roll in defeating and subduing the two powerful legendaries.
This pattern of Aero going to pokemon league's fighting crime, and capturing legendaries continues.
The stakes would be higher in situations where Aero is present, to balance out how straight-up powerful he is. He would also use different pokemon forms a lot.
Anyways Ash goes to the battle frontier, Aero goes off to Sinnoh. They meet up at some point, Steven experiments with some contests.
At some points, Aero would travel with Ash and give advice and help solve problems. He would probably watch Ash compete and would also totally kick Tobias's butt.
I'll probably finish the synopsis at some point, but you get the general idea. But I'll put an idea for the ending. Oh and somewhere the love interest/actually interesting character would be introduced. She would effectively be the female version of Aero. And would break out of a lab somewhere. Maybe even go out of control until Aero stopped her. That would be fun to write.
So things would probably reach a point, where the separate evil teams combine under Team Rocket to form this major threat to the world. At this point, Aero goes all out and gets seriously injured, almost dies, etc. But the world is saved. Aero retires after finally achieving his purpose and just enjoys exploring the pokemon world. Marries the unnamed oc, typical happy ending.
And that's it: Hope you enjoyed what could have been. Anyways if someone wants to write this out, feel free. I'd like credit for the ideas, but it's fanfiction. Have a good day/evening/night!