I had a few of these...
I'd put the Great Giana Sisters into Super Mario Bros... so they could have an epic confrontation the likes of which can only be captured in a flash movie.
I'd put Master Chief in Tomb Raider so two of my least favorite characters can kill each other once and for all. Two birds with one stone.
I'd put the entire casts of Final Fantasy VII, X, X-2, and XII into Tao Feng: Fist of the Lotus so they too could fade away with it into obscurity.
I'd take Dr. Ivo Robotnik from the classic Sonic games and put him into the modern 3D Sonic games, then I could at least correct ONE FUCKING UNNECESSARY AMERICAN CONTINUITY RETCON! (If you don't get the joke, don't say anything)
I'd put Sonic into a completely 2D version of any of his last three games. Then they'd be good.
I'd put Bubsy into any Spyro, Crash Bandicoot, Ty the Tasmanian Tiger, Ratchet and Clank, or Banjo Kazooie game so he could viciously murder them... because if there's going to be one king of the third rate mascots, it's going to be BUBSY THE BOBCAT!