First and foremost, I had a dream back in March or April that Beddy-Byes, a boss Yo-kai from Yo-kai Watch 3, was a playable character in Smash. Even as someone who doesn't really care for third-parties in Smash, the idea was so cool that I made sure to develop a moveset for her when I woke up. Not sure if I still have the moveset, however...
Other than that, Sutte Hakkun as a retro representative for the Super Famicom's Satellaview would be pretty cool. He could set up different moving blocks to block the movement of his opponents, as well as boosting his recovery. That'd be pretty interesting.
Kururin from Kuru Kuru Kururin would also be awesome, although I don't know what he would do, other than fly around in the Helirin. I just really love Kururin Paradise, and wish that Nintendo/Eighting would make a new game (and bring it to the States, for crying out loud).
Pretty much everything I just said for Kururin can also apply to Jill from Drill Dozer and Starfy from Densetsu no Stafy/The Legendary Starfy (they'd be cool, I love their game, and Game Freak/TOSE needs to make a sequel ASAP).
Pokemon-wise, Xatu, Manaphy, Pheromosa, Sableye, and Whimsicott are all favorites of mine. Of course, none of them will ever happen ... which is why they're here.
Part of me would also love to see a playable Dr. Kawashima. He's got the sales (And, by extension, recognizability) to make some sense, but since he's literally the floating polygonal head of a real-world doctor, perhaps Assist Trophy status is best, haha.
Also, a Bulborb from Pikmin. Imagine a giant strawberry-shaped grub thing stomping around the stage. That'd be great. Might not be the most popular choice, but it's pretty iconic, just not to the same level as Olimar or the Pikmin themselves.
As far as third-parties (that aren't random bosses from Yo-kai Watch), the Prince from Katamari Damacy. His costumes could be a few of his Cousins. I'd love to be able to play Smash as Foomin or Nutsuo, haha.