I wouldn't get hopes up too high, trophies don't mean a whole lot. The reason Mega Man probably doesn't have many is because there's not a recent 3D Mega Man game to pull models out of. In Brawl, most of the trophies were things from recent GCN/Wii games or Brawl itself; that's why they were able to put so many. If a character doesn't appear in another form it's not out of the realm of possibility that they didn't want to take the time to model them just for a trophy.
That said, Ridley will obviously be in the Wii U version in some form, and they've been coy enough with him that I wouldn't be surprised if he's playable. Isaac not appearing at all would be strange, but not terribly surprising. Bandana Dee not getting anything wouldn't really surprise me at all though. I don't know a lot about the character, but I'd be surprised if Kirby got another rep with Kirby, MK, and Dedede already in the game, and there are a lot of beloved/important characters who don't get trophies.