Wow, this wall of text is extremely daunting. There were a few points brought up / changes suggested that I'd like to respond to. These points are not terribly important, but they stand out to me since I'm a Jigglypuff main.
What I would like most is not the addition of a lot of new stages (though Warioware is great), its the widespread acceptance of the "borderline" stages. We'll make more progress by fixing up iffy stages than revamping banned ones. Those stages are meant for drunken FFAs anyway.
1.
The cars on Mute City Aero Dive: I can't see many people objecting to removing them, and I honestly can't see it as a counterpick otherwise. While the cars are certainly avoidable, they really disrupt the match and can just flat-out KO a person not familiar with the stage. While its easy to say, "It's their fault for not knowing the stage." the stage isn't generally CP anyway so how many people actually know it well?
Removing the cars or tremendously reducing their knockback will make this stage more... palatable to most people, and it truly is a really interesting, unique stage. I would love for it to be consistently legal. Booo car Johns!
2.
Jungle Japes: the klaptrap, like the cars, is completely predictable. It appears every 10 seconds on the 7. H***, I float all around it as Jiggs. Its way less of an issue than the cars... BUT people hate it. I don't think it needs to go entirely by any means.
The above applies to the friendly, lazy, and docile klaptrap. The psychotic jumping klaptrap is another matter entirely. By which I mean, slightly more worth removing, as it is waaaay more dangerous and its movement is less predictable.
3.
The water flow on Japes: its speed could be lowered, but the water is supposed to be scary and hostile. I mean, it has a f***ing gator. Definitely not something that has to be changed in a counterpick stage.
4.
The bulborb on Distant Planet: If you feed someone to the Bulborb, it is profoundly satisfying. If you randomly get eaten by the bulborb, you are an idiot. Basically its about as bad as leisurely strolling into a reverse-warlock punch.
The lack of auto-sweetspotting makes it more possible to use the bulborb, but seriously, in competitive play...
Leave the creature alone!
5. The rain on Distant Planet.: should be on continuously, and slowed down somewhat. Walk offs of any kind should still be avoided, especially given Pikachu's ****-throw.
6. A bazillion stages: It would be hard to make stages legal without risking homogeneity. It would also wreck the CP system, as Chibo pointed out. On the other hand, if the snazzy coolness of some of the banned stages was left intact, it could be worthwhile. Having something that offers genuinely new and varied options would be great, but we don't want a bunch of clones.
7. The Waiting Room: bears a startling resemblance to another flat, platformless neutral stage. This illustrates the problem for the CP system pretty well.
Its a little intimidating here with the caliber of posters... but those are my initially thoughts, I'll post more soon.