Well that shouldn't be an issue. There are people who know only Digimon, or Yu-Gi-Oh, or Pokémon, or some other genre franchise and believe everything sprouted forth from that wellspring, and that anything even remotely similar is "a rip off." These people will either figure out someday that no franchise invented everything and that most of the genre tropes sprang forth from properties that predate these by decades... or they won't, and they'll keep screeching about "RIP OFFS!!!!!!!1" Either way, you can't account for these people and you shouldn't worry about them.
The bigger and more important note is simply that in a franchise where evolution is MOSTLY permanent, the concept of fusion is impractical as far as gameplay and mechanics, to the point where there's probably no end of reasons why they've never really touched upon it.