Is it really ruining it though? Or is it just different?
Ignoring the obvious problems of unfinished plot threads and lack of familiar characters, what makes the post-reboot story worse than the pre-reboot story? Is it really bad that the comics are similar to the games? I wouldn't say so, I'd say keeping the comic canon closer to the videogame canon is better because it's much easier for someone who enjoyed the games to jump into the comics. There's no fussing over whether something this game happened in the comic, or whether this character did this in the comic but that in the game.
Like the Unleashed arc that's happening now, I very much doubt they're going to stray very far from the videogame canon. A few details here and there will be different, like Sonic getting a face full of Gaia-gas instead of getting zapped by Eggman, for instance. All the major changes I imagine will be relegated to the comic adding things rather than changing them. There will be more stuff happening that's unique to the comics but the major points of the games will remain the same. Sonic turns into a werehog, the world is broken up, Dark Gaia is released, Chip is released, Chip helps Sonic & co use the Chaos emeralds to put the world back together while Eggman gathers Dark Gaia into a single place, and then Chip and Super Sonic will smack Dark Gaia around until it goes back to sleep. I can pretty much guarantee that all of that will still happen, it'll just have more in-between.
English