Ending Mario would be easy. Just have him go get a different girlfriend. I mean, surely there's another princess in another castle that can, er, make cake as well as or better than Peach.
Zelda? Hasn't that ended, like, fifteen times now? End it without making another one.
Metroid? Have Samus find a decent fellow, make a couple o' babies, and imprison Ridley then eject that shit into deep space where no one will find him.
End Pokemon by having an in-game PETA-like organization that brainwashes everyone into thinking that capturing animals in tiny balls and making them fight each other is actually a bad thing.
(Yes, I know something similar exists, and I know it's wrong, but I can't think of a better way to put it)
End... uh... what have I missed?
Also, refuse to make anymore freaking prequels.