OK, how's this for an original game...
Sonic gets captured by a rouge Metal Sonic, and this time it's not Dr. Eggman's fault. Metal Sonic causes lots of destruction to the planet with his army of robots, and Eggman is distraught because his creation is no longer loyal to him, and his dream of taking over the world will not come true if Metal Sonic destroys it. Eggman thus decides to help the remaining heroes by teaming up with them, supplying them with equipment and weapons. Here's a list of the character's roles...
Doctor Eggman/Robotnik will be a supporting character, who can supply you with upgrades for your characters. Upgrades will include more health, better damage, tech, and new combat moves.
Tails, being the genius he is, stays behind to help the Doctor with the upgrades. Players will get to play as Tails in certain areas, as he comes in a large battle mech that he has created. This would be more of a first person shooter, think Chrome Hounds combined with the Sonic Universe.
Knuckles travels the planet with Rouge to find the Chaos Emeralds. This will be more of a 3D platformer, with a boss robot guarding each Chaos Emerald.
Shadow, feeling that it is his duty to protect the planet and keep his promise to Maria, goes straight for Metal Sonic and his army. His goal is to destroy Metal Sonic, free the "Faker", and rub it in his face.
Amy tags along with Shadow to save Sonic. Shadow and Amy gameplay will be similar to the gameplay of the God of War series. (Insert ShadAmy here)
Sonic eventually breaks free of his confinement and starts destroying Metal Sonic's base from the inside out. This would be more along the lines of a Splinter Cell/Assassin's Creed game, but sped up. At the end of the game, Knuckles and Rouge give him the Emeralds, allowing him to go Super and beat Metal Sonic.