Here are my thoughts. My decisions would change with time, as the more time the PMDT have, the more potential the PMDT have with unique stages.
Page 1
Skyworld = Brawl Skyworld(breakable platforms and stuff)
Hyrule Castle = N64 Hyrule Castle(Confirmed)
Metal Cavern = N64 Metal Cavern(Confirmed by PMBE Member)
Bowser's Castle = Hazardless Bowser's Castle
Saffron City = N64 Saffron City(Confirmed by PMBR Member)
Peach's Castle = N64 peach's Castle(Confirmed by PMBR Member)
Infinite Glacier = Brawl Summit(Confirmed)
Lylat Cruise = Melee Venom?
WarioWare(now AshleyWare) = Brawl WarioWare(with mini-games)
Fountain of Dreams... I got nothing.
Final Destination = Brawl Final Destination(hopefully with fixed siding)
Yoshi's Island = Seasonless Yoshi's Island?(Seasons don't change)
Distant Planet = Brawl Distant Planet(pretty much confirmed)
Norfair = Brawl Norfair
Yoshi's Story = Melee Yoshi's Island? N64 Yoshi's Island? (A re-made Melee Yoshi's Story would be beautiful, but I am not too sure if they would do that.)
Green Hill Zone = Brawl Green Hill Zone(Confirmed)
Smashville... I got nothing, so I am going to roll with the 24/7 K.K. Slider idea.
Battlefield = Melee Battlefield(Confirmed)
Pokemon Stadium 2 = Pokemon Stadium 1(with or without hazards?)(Confirmed)
Delfino's Secret (A.K.A. Dracula's Castle) = Delfino Plaza(Confirmed)
Dreamland = N64 Dreamland(Confirmed) (Personally, I would have liked a competitive Green Greens, but I don't mind the N64 Dreamland.)
Page 2
Shadow Moses Island = Pillarless SMI?
Kongo Jungle... I got nothing, considering Jungle Japes and Rumble Falls are already on the menu. Maybe Melee Kongo Jungle.
Fourside = New Pork City (Sadly. That stage was... Just... No.)
Onett... I got nothing.
Big Blue... No idea.
Port Town Aero Dive = Melee Mute City(PLEASE PMBR!) If not that, maybe Neutal/Frozen Port Town Aero Dive.
Flat Zone 2 = Flat Zone 1
Luigi's Mansion... I got nothing.
Jungle Japes... Maybe Waterless Jungle Japes? Or Melee Kongo Jungle is it wasn't under N64 Kongo Jungle.
Corneria = N64 Sector Z(Basically Confirmed from Art Sunday Imgur)
Brinstar = N64 Planet Zebes(Basically confirmed from Art Sunday)
Temple = Skyloft(It doesn't appear on the menu, so that's my guess.)
Pirate Ship... I got nothing.(I personally don't think Melee Great Bay would make it in, but I don't frown upon the idea.)
Spear Pillar... I got nothing.(I don't think they would make a Poke Floats. However, I don't frown upon the idea.)
Training Room = Brawl Training Room(Maybe with platforms...)
Rumble Falls = Brawl Rumble Falls
Halberd = Halberd with Hazards(That's my guess at least.)
Frigate Orpheon = One-sided Frigate Orpheon(doesn't flip) OR Melee Brinstar Depths?(It's a possibility.)
Castle Siege = Singular Castle Siege (probably the first or thrid stage without transformations)
Hanenbow = Brawl Hanenbow(Hopefully something else.)
Pictochat = Brawl Picochat
Also, Alternate Stage Loader(minimized to ASL) has been a code since 2010? (approximately) and has last been caught working with Project M 2.6. It started glitching with 3.0, and I am SO happy the PMDT have worked this code into the game. Personally, I would have liked if they had certain stages with a "Press R + A" option, for another alternative stage, like N64 Battlefield and N64 FD.
EDIT: Confirmed from Nanobuds from the PMDT, not all stages are getting Alts. Mewtwo2000 is planning on updating his old ASL tool in order for it to work with Project M 3.6's codeset.