I yearn for the days of the Adventure games that gave you multiple perspectives of different characters and I feel like considering the era Sonic X was made in, it is fitting for it to follow that structure. What I struggle with is the playable character roster and the exact approach to the story.
I feel like Sonic and Shadow would have to be playable in separate campaigns, that much is obvious. The problem is the other characters, season 3 is very much a "Sonic and his friends travel as a unit" type of story and considering it takes place in space it would not make sense to separate them. But I also don't want to sideline the others, especially Tails considering his and Cosmo's story is basically the emotional center of that arc (and my personal favorite thing about it), but I have no idea how I would incorporate Knuckles, Amy, or Cream. Rouge would probably accompany Shadow as usual (I would change it so that Shadow is not revealed to be alive in this game for chronology's sake), probably joined by Omega as well.
That's still 9 whole characters, with Team Sonic having 6 characters and Team Dark having 3, so it's out of balance. Of course you can split Team Sonic into two, but the character selection would not be the usual Sonic/Tails/Knuckles because like I said, Tails and Cosmo's story takes priority which means it wouldn't make sense to separate them. (I'm not even taking the Chaotix into consideration assuming I choose to incorporate them)
The setup I had in mind was this:
Sonic's story - Sonic, Knuckles, Cream
Shadow's story - Shadow, Rouge, Omega
Cosmo's story - Cosmo, Tails, Amy
It's not traditional at all, but I feel like Sonic and Knuckles babysitting Cream would be a funny dynamic and I like the idea of Amy playing wingman to Tails and Cosmo, it's cute. But then there's the question of why would Sonic and Cosmo's groups split up (it would make no sense to give them two separate stories if they're together).
There's also how everything ties up thematically - Sonic and Shadow are pretty obvious to me, as Shadow would end up acting more heroic while Sonic shows a taste of his inner darkness as Dark Super Sonic, but Cosmo doesn't exactly serve as a great middle ground between the two as far as I can remember. Of course I have to rewatch the show before I actually write the story (and the game itself will not be ready for a couple years) but I felt the need to scream into the void.