It could be true that Atlus being a Sega subsidiary may not have mattered, but I'd argue that it probably helped at least a little bit, as Nintendo would have known ahead of time that negotiations for him would be a breeze based on Sega's previous involvement with Smash.I don't think Joker is in because Sega owns Atlus. I think those two things are completely unrelated. So I wouldn't expect anywhere near this much double or triple (or quadruple) dipping from third party companies.
As for the others, I don't see why Capcom wouldn't get a third unique rep since they have a massive catalog of popular characters to work with and seem to be the easiest third party to work with of them all, and meanwhile, Namco (who's helping make the game) only has one rep while even Square is likely getting a second, so it's reasonable to assume that they could get another as well.
For my Wild Card, if no one double dips any further and it isn't Pokemon or Fire Emblem, either Level 5 or Tecmo Koei would have to be my best guesses as for what companies that the character would come from, which would get us either Ryu Hayabusa or Jibanyan.