This is part of the problem with Sonic...some of these games have taken the stories way too seriously...we're talking about a blue super fast running hedgehog here...any attempt to be taken seriously comes off as super ultra #1 cheese fest (examples: Shadow the hedgehog, Sonic The Hedgehog on PS3 and 360, Sonic and the talking Sword crap game, and so on).
I say keep the story simple and retro and give us amazing levels. Just keep the story as it was in the 2D days...Robotnik captures animals, puts 'em in robots, and tries to get the Chaos emeralds. Sonic saves animals, get's the emeralds, becomes Super, and kicks ass. It's a tried and true formula...why deviate? For christ sake, Mario has been running on the same formula since game one and those games are still really really good.