Neutral (6):
Final Destination
Battlefield
Smashville
Lylat Cruise
Yoshi's Island
Pokemon Stadium (Melee)
Potentally Neutral (3):
Delfino Plaza
Castle Siege
Halberd
Counter-Pick (13)
Norfair
Pictochat
Mario Circuit
Luigi's Mansion
Great Sea
Distant Planet
Frigate Orpheon
Green Greens (Melee)
Corneria (Melee)
Onett (Melee)
Brinstar (Melee)
Rainbow Cruise (Melee)
Potential Counter-Pick (7)
Shadow Moses Island
Green Hill Zone
Haenbow
Pokmon Stadium 2
Eldin Bridge
Jungle Japes (Melee)
Yoshi's Island (Melee)
Banned (14)
Rumble Falls
WarioWare
Skyworld
New Pork City
Summit
Mushroomy Kingdom 1-1
Mushroomy Kingdom 1-2
Port Town Aero Dive
Mario Bros.
Spear Pillar
Flat Zone 2
75m
Big Blue (Melee)
Hyrule Temple (Melee)
Congratulations, sir, this is the first stage ban list that I agree with, or come very close to agreeing with. I would definitely call Delfino Plaza neutral, and probably Castle Siege too. None of the transformations are very disruptive at all on Plaza, except maybe the one with a walk-off edge. Even there, playing defensively would probably be sufficient to avoid Dedede until the stage changes. Castle Siege's middle form is the only questionable one: it has walk-off edges and statues that inhibit projectiles. My feeling, for now, is that neither of those features will be all that disruptive.
I think that Jungle Japes will be counterpick legal. The water is much more forgiving, although Ike has major issues in it (in fact, I think that he would have done better with the old water). Additionally, it is easier to avoid the water entirely because everyone is floaty. While moving water is too harsh on Ike for a neutral stage, it was counterpick in Melee and is more fair this time around.
I'm not sure about this, but for now I have no serious issues with Shadow Moses Island (as a counterpick stage). Wall combos are not really more of an issue than in Melee, and Green Greens was counterpick. The stage is perhaps unfair when the walls are destroyed, but that doesn't last long and takes some effort. It drastically favors characters with good vertical KO power (and Kirby), but hey, a giving some characters a significant advantage is a textbook example of a reason to make a stage counterpick-legal.
I think that the layout on Yoshi's Melee Island makes it difficult for Dedede to chaingrab characters off of the edge, and I know that it makes backthrow camping very difficult. With the blocks to disrupt projectiles and the close boundaries, this stage is certainly not neutral, but I don't think that it deserves to be banned. I'm not completely certain due to the left KO boundary, but I'm confident enough that I would put it on the counterpick list.
Green Hill Zone is, in my experience, very campy. Backthrow camping is very effective on both sides, and can easily make a game degenerate into a stalemate, and the center provides a situational but sometimes very large positional advantage. In Melee, I believe that easy backthrow camping was considered a ban-worthy offense.
The only stage that I really disagree with you on is Great Sea. The hazards are very predictable and the advantage to aerial characters only applies for a short period of time. I understand that this has been discussed, and I understand your position, but I happen to disagree with it. I think that Great Sea should be potentially neutral, with Halberd.