I can pretty much run through why every stage that isn't coming back isn't with reasonable speculation:
Planet Zebes: Probably seen as redundant with Brinstar. It really isn't at all, but that's how it's commonly looked at.
Sector Z: Literally just a bigger Corneria without the main gun.
Icicle Mountain: This stage would be a huge burden to actually implement (it's a ton of geography and art to make), and it played extremely badly in the opinion of basically everyone.
Mute City: Actually a bit of a surprising omission. Again it's a pretty big stage if you consider the total area you tour past so it would be more work than a typical stage, and it might have been viewed as largely redundant with Port Town Aero Dive.
Mushroom Kingdom I: This stage would be relatively easy to implement, but the aesthetic really overlaps Mushroom Kingdom 64 except with none of the charm. This stage is extremely low quality no matter where you sit on the casual-competitive spectrum and likely absent for that reason.
Poke Floats: A pretty big "loss", but this stage was very large and therefore a lot of work to make. Especially problematic may have been that, as a tour of the Pokemon world, it was laser focused on the first two generations as those are the only ones that existed in the Melee days.
Flat Zone 1: Absorbed by Flat Zone X
Rumble Falls: Basically the same story as Icicle Mountain. I think it's very deliberate that this stage design style disappeared in 4 and hasn't come back.
PictoChat 1: They probably felt that having the same stage twice with different transformations was worth it for the popular Pokemon Stadium stages but not for the less popular PictoChat stages. Unfortunately, I think most of the community would agree they picked the version with far inferior drawings.
Flat Zone 2: Absorbed by Flat Zone X
Rainbow Road: Touring stages are again extra work (especially one as colorful as this), and this stage has the secondary downside of just being a much worse designed touring stage than all of the others from a gameplay perspective minimizing the value of putting in the work.
Pac-Maze: The 3DS gimmick associated with this stage must be something they couldn't come up with a satisfying method to translate to single screen play.
Jungle Hijinx: The background mechanic probably made a lot of problems in a lot of ways; it's kinda a QA nightmare. Stage Morph in particular raises serious questions about how it would work on this stage.
Pyrosphere: They must have perceived that having a double dose of Ridley would be awkward and that this stage wasn't worth keeping without the boss Ridley.
Woolly World: It seemed like a strange stage to cut at first, but the yarn textures and the stage's oscillation may have been considerably more taxing on the Wii U's CPU than we realized. This stage was limited to 4 players only, and very "heavy" stages are likely cut to play nice with Stage Morph and 8 player smash being on every stage.
Orbital Gate Assault: Without a doubt the single most taxing stage on the Wii U, this stage was assuredly cut for performance issues with the features they were introducing in Smash Ultimate. Its general lack of popularity no doubt made this an easier decision.
Miiverse: Obviously the Miiverse no longer exists so this stage lost its purpose. We certainly have enough Battlefields in this game.