To start, ones I think are sure bets for inclusion are Peach's Castle 64, Kongo Jungle 64, Yoshi's Island (Melee), Brinstar Depths, Delfino Plaza, Rainbow Road, Paper Mario, Dream Land (3DS), Wooly World, Jungle Hijinks, Gamer & Windy Hill Zone. These all are obvious choices for inclusion in some form as none really conflict with other stages.
I'm actually so-so on Fountain of Dreams despite my love for it. Depends on whether they can get the reflections to work properly or not. If it's in the game and they haven't shown it off yet, this is potentially why.
Pokefloats I'm also 50/50 on. It will of course need to be redone from scratch (then again it seems like all the Melee stages are this time around), but I don't know if Sakurai thinks the Pokemon used on the stage dates it in any way. I'd personally love to see all the original Pokemon with new ones added as well.
I honestly doubt that Mushroom Kingdom 64 will be included. The Melee version fits better with how retro stages are done now. However, Mushroomy Kingdom is also a thing, so maybe that's going to be this game's SMB1 stage.
As is well known, Planet Zebes and Sector Z were essentially remade into Brinstar and Corneria respectively for Melee, leaving the former 2 obsolete. Since Brinstar is confirmed and Corneria (or something similar) seems to be in the game I don't see those 2 N64 stages making the cut. Can definitely see the N64 music included though for their appropriate stages though.
I actually would be quite surprised if Rainbow Cruise, Icicle Mountain or Rumble Falls made it in. Sakurai seems to no longer like those kinds of stages (although Big Blue is in so IDK). Guess we'll have to wait and see.
Mario Bros. has the POW block. Not an immediate reason for disqualification (just because an item is also on a stage doesn't mean that stage can't exist) but it hurts its chances for sure.
Pirate Ship really depends on if a certain fighter
makes it in with a certain stage as well. Shame if it isn't as I've always kind of liked it and loved it's Omega form in 4.
Hanenbow would only get put in if Sakurai really wanted to.
Mute City is iffy as there's both the Melee and 3DS versions. I personally want to see both, but some have apparently spotted the Melee version so that brings the 3DS version in doubt for the time being.
Golden Plains and Pac Maze are probably out due to gimmics, a real shame in the latters case.
Big Battlefield will likely be redesigned to match the new SSBU Battlefield, but that would make it a new stage.
Finally as for Miiverse, yeah, no. Although I too will miss the inappropriate memes LOL. Also with all stages getting Battlefield forms it's slightly redundant at this stage, at least more so than Dream Land 64, Yoshi's Story and Midgar.