I think that part of the problem is that once you make one exception, it's a lot harder to justify not making more. Imagine how rabid fanbases would have gotten if, during Brawl, Snake was the only third party character, or if they didn't add any new third party characters in future games and just left it at Snake and Sonic. (I'm sure some people would claim that's ideal, for reasons that I cannot fathom, but that's not what I'm getting at here)
Fanbases for characters like Mega Man would erupt, pointing out that someone like Mega Man makes just as much sense (if not more) as the third party characters that got in Brawl, so why should he be excluded?
Now extend that to every form of media - people could say "if Goku got in, why can't (Spider-Man/Mickey Mouse/Batman/Spongebob Squarepants/Harry Potter/Naruto...)?" It would never end.