Okay, I haven't read the whole thread (22 pages is a bit much to ingest), but here's my take on this ban list. Keep in mind that I'm a scrub looking to work into some tournaments down the road, so my views may be a little off-base, as I'm not used to how all the tournaments work exactly.
The neutrals are all fairly cut dry: flat stages with no outside interference. I see no problems.
I don't totally understand what a counterpick is, exactly, but what I'm guessing is a stage you pick to give your character an advantage over the others. I'm not sure why it's separated from the other legal stages, but I guess that's why I'm not making the lists. I've seen debate about a few of these, so I'll put in my two cents on a few.
Castle Siege
I think this should go neutral. The only thing that really could peg it down a bit is the fact that there are walk-off edges during portions of the stage (which may be enough to bump it into the realm of counterpicks).
Great Sea
Keep it there. Maybe I have some favoritism because I'm a big fan of the stage, but nothing seems to come out of nowhere completely. The storms are all very obvious due to the change in the background, bombs can be seen coming from behind, and a word bubble comes up when the ship crashes. Basically, all the subtle changes are accounted for in the stage itself. The only issue is the spring, but that should just be avoided. If you're willing to take the gamble and walk around it when it's set, then you shouldn't be complaining if it sends you flying.
Battleship Halberd
Keep it on; there's no real reason to ban it. All of the hazards are clearly visible and avoidable, which makes getting hit by one really on the fault of the player and not the stage. The issue with the takeoff also shouldn't be a problem, as it hasn't had an impact on myself or my friends yet, despite our having had the game for only a few days. If the players know to expect the floor to drop, they simply shouldn't allow themselves to get caught.
Green Hill Zone
Not a favorite of mine, but I agree that it should stay as a counterpick. As I see it, counterpicks are stages where something about them can change, which makes them not-quite-neutral, but also not so bad that they should be banned. The minor changes in Green Hill are small enough where the only real concern could be the walk-off edges, and even these aren't too disruptive.
Now the banned stages... the list looks mostly good, but I feel the need to comment on the stages.
Mushroomy Kingdom
Good, keep it like this. Scrolling and walk-off... all you need is a cheap Pit player to spam the side B on one of the walls and you have a KO.
Mario Circuit
I think it should stay in. The karts aren't much of a disruption from what I've noticed; when they come overhead it's clearly marked and when they come from behind you can clearly see them approaching. The walk-off edge may be an issue, but I don't see it as enough to ban unless a meta-game evolves to the point that it becomes broken (like a WaveShine).
Bridge of Eldin
Basically the same as Mario Circuit, but this time with the charging guy. It's not hard to avoid him and the exploding bridge is painfully easy to avoid. The only issue, again, is the walk-off edge, but I don't see that as a big issue just yet.
Rumble Falls
Keep it banned. I like the stage and think that it might have a shot as a counterpick, but it really has too much to keep up with, especially with all the spikes scattered around the stage.
Norfair
Haven't played on it enough to really say anything...
Pokémon Stadium 2
I'm not really sure why this is up as a banned stage. Would someone care to explain? Nothing seems overly broken, as all the disadvantages are applied to all the characters equally.
Port Town
Haven't played on it enough to really say anything...
Wario Ware
Love the stage completely, but it can't touch tournaments. There's the fact that winners of minigames can get random prizes and that you can take out a player trying to win too easily (a friend of mine was standing still during that game, so my other friend promptly charged up his Ike FSmash).
Distant Planet
This one should stay legal, I think. I may be totally underestimating walk-off edges, but that's really all it has going against it. When it rains, just don't touch the angled platform; even then a recovery isn't terribly difficult. Likewise, when the monster shows up, just don't jump in its mouth. Not too hard to do, right?
New Pork City
Good riddance. Miserable stage.
The Summit
See New Pork City.
Pictochat
I think it has a good shot as being a counterpick. The only concern, of course, is that there's no control over what comes up.
Shadow Moses
Sad to see this on here, but because of the infinite combos that can be done on the pillars and the walk-off edges, I suppose its inevitable... =(
DK Arcade
See New Pork City.
Spear Pillar
Probably my favorite stage in the game, but as with Shadow Moses, I see why it must go. There is just too much random stuff going on to make it playable. My favoritism makes me consider that it could be a good counterpick, as the beams are easy to avoid and the inverted controls can be learned by players, but I don't see that argument going anywhere.
Mario Bros.
See New Pork City.
Flat Zone 2
Better than the last one, but still miserable. Small ceiling, walk-off edges, lethal hazards. Does it get any worse for a tournament player? Oh right... the DK Arcade...
Electroplankon
Why's this one on here? The stage is a bit strange, but there's nothing out of the ordinary going on. The leaves move around but only if struck and not enough to make that a devastating kind of hazard. Maybe an explanation?
That's it from me... I may have underestimated the power of walk-off edges, but they just don't seem, at this point in the meta-game, to be very unfair. Feel free to correct me if I'm wrong, though. Hopefully I don't have too much of a "casual" gamer mindset infiltrating this list.