It seems like, for the most part, characters who aren't from series directly made by Nintendo (aside from third-parties) aren't really getting in. There are very few characters in the game who aren't from primarily first-party series, and Sakurai said recently that even Pokemon is like a weird exception because it's not 100% Nintendo. I think it's kind of unlikely that games like Golden Sun and Xenoblade will get characters in the game, even though they've sold really well.
I don't really care much for Golden Sun, so don't take this as me trying to argue for the series, but I think it's kind of odd that Sakurai said something like "jeez, there aren't very many post-Pikmin Nintendo games I could pull stuff from" on the Dojo when Golden Sun sold millions of copies. That's probably a sign of something.