The one thing from Sonic 3 that irks me is the erasure of Maria's disability as it's a big part of her story in the games. It could have been a good talking point with kids and their parents irl about illnesses, like how her death (she still gets violently mirked by GUN, just in a slightly different way) could be. I haven't even played the games, the movies being my main introduction to the franchise, but I did find out about Maria as well as Shadow's backstory in general through fandom exposure since the first two movies.
Sure, the writer's excuse could be "it isn't relevant to the plot" or "it's not supposed to be exactly like Sonic Adventure 2". But it still wierds me out that they included Maria but not her illness (that appears to be debilitating and would lead to death), which good or bad is a whole thing in her very short involvement in the game's story. It feels like taking away Tails' extra tail or Sonic's personality. Not to mention ableist.
So screw it Sonic 3 AU where pretty much everything is the same except Maria has her illness/disability.
Let's say there's a flashback where Shadow and Maria are playing as usual when she suddenly coughs and/or faints. Shadow tries to shake her awake (could be another foil later on when Sonic tries to wake Tom up after Shadow hurts him) when Gerald and the other scientists reach them.
Next shot or flashback for Shadow is him standing outside Maria's hospital room in the bases' infirmary (do military research bases have these? Idk. Let's say so for this AU) seeing her passed out in bed hooked up to machines and ivs. Gerald comes up to him and explains Maria's illness and that he brought her to the base because he thinks that the research they're doing with Shadow could stabilize or even cure her. Shadow agrees to do whatever testing is needed to help his friend/sister.
And the research actually helps ease Maria's symptoms and improve her quality of life where her and Shadow can play more often. But there are whispers between Gerald and some GUN agents that this is at the cost of the initial weapons research on the edgehog-to-be (please let me know if this wasn't what they were collecting his power for) and it turns into a verbal argument that both children can hear. Gerald notices and storms off to shoo them away or tuck them into bed or something.
Maybe on that infamous night Gerald was planning to leave the base for good, taking Maria, Shadow, and all the research related to him, with him all because GUN was shutting down the research that would benefit Maria to focus more on the initial goal of Project Shadow. Maybe they were shutting it all down due to a lack of results for the project's initial goal and not giving a crap about the side project for Maria.
Or maybe that night Gerald knew that GUN wanted more projects from him (cough cough, the giant nuclear space lazer station in the final act, cough cough) and he refused to give it to them for whatever reason (maybe hubris, I like to think that he had a lot of that in the movie before Maria's death and that this was a fatal flaw that indirectly resulted in it). So he tried to leave, taking just Shadow and Maria with him.
Maybe Maria's side project is why some of the GUN agents were willing to shoot her. Or maybe they were just heartless assholes, idk.
Maybe in the events after the movie in this AU, Stone meets up with Shadow and helps him continue "Project Maria" to help other children with the same illness in her memory.
Please let me know if I got anything wrong, I only saw the movie once so far and don't want to get anything wrong about the initial game's plot, as well as the movie's plot, or come off as ableist myself.