What I'd kind of think would be fun is if the bosses in the next game act like fusions of already established bosses. What do I mean that? Say the next big baddy is some type of weird thingamajig that can fuse things, so that our generic enemies turn out to be koopa/morblin hybrids or something like that. Bosses would be somewhat the same, so if say Pikachu and Samus team up again, the boss at the end of the level could be a fusion of Kraid/Magnezone (Magnezone chosen here so that the Kraid fusion would look kind of like what he would have looked like if he had gotten into Metroid Prime) or if Little Mac and Olimar team up, you could see a fusion of King Hippo and Emporer (or Empress) Bulbax. That way I think a lot more could get covered and there wouldn't be a need of constantly trying to shove in a boss for every series. (And for the record, Kid Icarus could probably have a boss in Medusa)