Sector Z and Planet Zebes are fairly large stages that are outdone in their layout/gimmick by Corneria and Brinstar respectively. Love these stages to death as someone who grew up with 64, and it would've been awesome to have every 64 stage in the game for the first time since the original, but they're ultimately redundant and it's fine that they're not here.
Icicle Mountain, Orbital Gate Assault, and Rumble Falls are auto-scrollers that aren't all that fun, honestly. They cross the line of bringing the attention to fighting the stage more than your opponent, and that's probably why they were cut.
Flat Zone and Flat Zone 2 were combined into Flat Zone X as you said, so they're both technically present anyway.
Mute City and Pictochats both have outright replacements in Port Town Aero Dive and Pictochat 2; again, they'd be redundant.
No joke, I had to look up Mushroom Kingdom's layout because I couldn't remember what it was. And it's really similar to the 64 stage of the same name, which is probably why it's not here.
I think Pac-Maze had some functionality with the pellets thing that might not have played well outside of the 3DS set-up. There's still Pac-land, so it's not as if Pac-Man lacks a stage, but I honestly would've preferred it over Pac-Land.
Jungle Hijinx, Pyrosphere, Woolly World, and Miiverse all have something that clash with elements present in Ultimate and their own design. Jungle Hijinx has that weird background thing that wouldn't play ball with Stage Morphing, Pyrosphere prominently features Ridley as a giant boss and was likely removed to not confuse the layman. Miiverse's primary functionality as a display area for Miiverse posts is now moot because the service has been shut down, and Woolly World is... actually, I don't know. I was thinking the Stage Morph thing might not have played well, but then Castle Siege is in the game, so I don't know.
Poke Floats is based on old designs and proportions and consisted of models ripped straight from Pokemon Stadium and the like. Normally this isn't an issue, as the stage could be remade with new assets, but I'm not sure there would be a way to completely re-create the stage with the newer designs, and the Pokemon Company probably has enough of a say on how their property is portrayed that Poke Floats would have to change too many of its own elements for it to retain its exact layout. If this stage would return, it would have to be a successor based on the updated designs and larger Pokedex.
Rainbow Road would look great in HD and probably the only one I'm sad isn't in the game. There's nothing that's preventing its inclusion redundancy-wise or design-wise, except that it's unmistakably based on the Mario Kart 7 Rainbow Road and they'd likely want Rainbow Road to prominently feature 8's version instead.
