So basically prior to three Megaman was dead? Well there you go. It's a bit sad, but lately he's been more hype than pay off in general. Even happened to the Megaman inspired Mighty 9 which I remembered for awhile received A LOT of praise and hype... And then it got closer and closer to release.
That doesn't even make much sense considering that Megaman can HARDLY be a shoto clone(Projectile and physical anti air, yeah, a lot of characters have those though, Megaman was more than unique enough to not be considered a shoto clone. Zero also has both of those things anyway, it's just that his moveset his more engaging.), TBH. I never really got that, that isn't really the problem people really had with MvC Megaman, the reason why I hear people don't really care for that Megaman is that he's pretty dorky. Though I myself just don't find his moveset as interesting as other characters, it's not that I have a problem with him, I just don't think he's as required as people think, especially since at the time he was pretty much dead, and still is dead despite any attempts to revive him. I just don't think Capcom was on a Megaman hate rampage like people think and rather they just realized that he's dead and that attempts to bring him back keep failing. It reminds me of how some Ridley fans think Nintendo personally hates Ridley, because in their minds they think that he has every reason in the world to be in Smash, but Sakurai and Nintendo see otherwise.(And this is coming from a Ridley supporter.) I mean, the fans could be right, however, it's good to consider what's going through the producer's mind too, who see things A LOT differently than fans do.
And I say that for Zero because he's been used in crossovers before mvc3, all over X too.