I think the problems with the story of Shadow Generations are two-fold:
1. It exists to be a commercial for the third movie (iirc Iizuka literally admitted that Shadow’s presence in the third movie was why they made the game).
2. It’s an apology/reset for Shadow’s characterization in the 2010s.
It doesn’t feel like the game was made because Sonic Team had an idea for a story and wanted to tell it. It feels like it was made to be an advertisement and to reassure fans that yeah, we know we fucked up Shadow’s character for over a decade, but we promise he’s better now! Please give us money again!
Like…they bring Maria and Gerald back but they don’t give them anything to do or have them experience any kind of character arc and I will never get over Gerald not being fat. They didn’t have any real ideas for how to use them; they just needed them there so newcomers know they exist and so long-time fans will get to see Shadow be nice to them and thus be assured he’s not a douchebag anymore.
They bring Black Doom back, but all he does for most of the game is troll, which doesn’t make a lot of sense. In the original game, he invades in the first cutscene and then is forced to bide his time because he needs the Chaos Emeralds. But in this game, he doesn’t seem to need them, so there’s not much reason for him to wait until Shadow is five doom powers stronger to start fighting him. He talks about wanting to take control of Shadow after he’s been perfected, but shouldn’t he already know that won’t work, since that’s what he tried to do in the last game and it failed? He literally admitted Shadow was immune to his mind control.
It couldn’t be more obvious that they couldn’t think of anything for him to do until the final boss scene. He’s only there to send Shadow to Radical Highway as an Easter egg for long-time fans and to tell new fans that he exists, in case they ever decide to use him in the cinematic universe.
Black Doom isn’t in the game because they had an idea for a story that involved him. Black Doom is in the game so that the Black Arms soldier can attack Maria so that Shadow can save her so that Shadow fans will breathe a sigh of relief that he actually gives a shit about helping people again and isn’t a one-dimensional asshole anymore. And, of course, so newcomers will see Shadow do something cool and thus want to see him in the third movie.
I get that Generations is “Easter Eggs and References: The Game,” but if you’re going to bother with doing a storyline, you should commit to it. The references should serve the story and instead it feels like the story exists to serve the references. Alternatively, it’s okay for it to not have a story! If they wanted to just make the game a compilation like they did with Mania or Sonic Mega Collection, that’s okay! I’m sure my nostalgic ass would still buy it. But if you’re doing a story, you should actually…ya know…do a story. Not just references and introductions and a commercial/characterization reset button pretending to be a story.
For all its flaws and all its bad ideas and plot holes, Shadow 2005 feels like they really did have an idea for a story and wanted to tell it. It doesn’t feel like a commercial or a Sonic Wiki page or an apology. That’s something I wish Generations had.