I believe that title is self-explenatory So here my idea: Sonic vs Eggman.
Two stories + Final Story. In both stories you can switch at any moment between fast character (Sonic/Metal) and flying one with gadgets (Tails/Eggman). Cream and Marine/Orbot and Cubot serve as tutorial/exposition/shop/comic reliefs. Eggman bots and Sonic friends as bosses. Bots and Blaze army/G.U.N. Forces as enemies. Big part of story takes place in Sol DImension. Blaze and Nega are final bosses. In Final Story you play as Eggman against Super Sonic and then as Sonic against Eggman machine powered by Super Sonic Energy (working name: Egg Champion). Fight starts with Eggman saying "Run, Sonic...RUN!" and that what you do cause robot is immune to your attacks. Its made of nanites and it simply fixes in seconds any damage Sonic can do to it. Eggman is inside of it in a capsule and he's directly hooked to nanites so Champion repeats all his moves. in first phase you must collect boost to knock Eggman out of robot, then he flies to his ship. Then you must chase after Eggman while avoiding Champion, until you both get to his ship. Egg Champion cant attack you without destroying ship so intead you must fight internal defences .(Think like final bosses of 8-bit Sonic 1 and 2 games but in 3D). Final cutscene showes Egg Champion comically repeating Eggman moves, when he throws a tantrum and tries defend himself from Sonic.