I think a lot of people forget that most Yoshis are generic, that every Pokemon is generic as well. That's why them being popular or notable in media(especially movies and the anime) is why they're chosen.
I do agree to an extent. I don't mind certain generic characters(Mii's, Yoshi, Pokemon, Link(he by design is meant to be your avatar in the Zelda games. Hence the chooseable name, lack of emotion and dialogue, very little similarities among each Link, sequels being an exception...), and I think that was it? I'm not counting Toad since while there's tons of them, there's a particular one that shows up who has a different coloration, and actually has a separate name in Japan. But you can count that too, sure), just as long as they have potential for a fun moveset. They should still be partially important. Mii is a normal protagonist in general, same with everybody else I mentioned as is. As for the whole "other Metroid characters work", I couldn't disagree more. Ridley is pretty much the only unique choice left. The rest besides Dark Samus are slight variants of Samus with their options, or would have little moveset potential in the end. The Hunters really were meant to be based upon Samus' gameplay with some slight variation. They're just more Falcos, something I want to see gone. More real variety. If they aren't going to be closer to Wolf, who barely qualifies as a clone, it's a waste of time. Also, let's not pretend they have a chance due to being too similar to Samus as is. I think Dark Samus had a chance if she wasn't an AT. Namely because she really isn't a clone in gameplay, just looks that way to the naked eye.