PokeFloats should've been brought back considering they remade a 2nd Pokemon Stadium anyhow. Though I prefer the original to the 2nd one, since the changes don't actually change the way a character moves, like the super floatiness change or the conveyor belt one in PS2. Saffron City would've been really cool to bring back, since that was one of my favorite stages in 64.
I loved Onett, so I have no complaints. I liked Fourside a lot too, would've been nice to see it back.
Temple was an excellent stage, especially for 4 players, and was definitely the best Zelda stage. Great Bay was also good, but it was too small for larger battles.
Green Greens was bland, and bad for me, since I played as Ness, and I could get trapped in the tiny holes, unable to recover with PK Thunder. Dreamland would've been awesome to return, since the music, along with the close quarters, made it really intense. It was also very neutral and had no major hazards. Fountain of Dreams was too dark and was a little hard to see.
Yoshi's Island was annoying with the rotating blocks. Yoshi's Island 64, or the other Yoshi's Island level, the tiny one with Battlefield style platforms, would've been better choices.
Rainbow Cruise was awful, considering there were so many better Mario stages. Peach's Castle was a good level, and so was the 64 level. I can understand why they brought back Rainbow Cruise, considering Peach's Castle was rather forgettable. Mushroom Kingdom was alright, as Mushroom Kingdom 2, but none of them were truly spectacular. Mushroom Kingdm 64 would've been cool, with the pipes, as would've the other Mario 64 stage, which I think, is the best Mario stage in all of Smash, close with Delfino Island.
Big Blue was a good choice, considering they remade Mute City into crappier Port Town Aero Drive anyway.
Jungle Japes was definitely not as good as Kongo Jungle, Melee & 64, but it's fine. The small side platforms are annoying, as the rushing water & klaptraps, but it's fun for big battles, with the tight quarters.