In Project M (and smash in general), the most well-designed and least exploitable stages are flat with a handful of platforms. This layout allows for a variety of playstyles and movement options from the cast without favoring any one character significantly more than the others. That's why the most played tournament stages are all "flat with a few platforms": They're the best for fair, competitive play.
Obstacles such as permanent walls make certain characters insanely powerful by providing infinite combos (which aren't very enjoyable) or huge camping potential (which is also no fun). No one wants to deal with a random laser cannon KOing them when money is on the line, just because your opponent chose Halberd instead of Battlefield. These stages are usually banned for that reason.
I know the bottom row of Page 1 looks incredibly bland (it has 3 "flat" stages and 4 "triangle" stages), but looking closer you'll find important differences between each stage that makes them unique. Compare the tiny size of Yoshi's Story to the much larger Dreamland: If your gameplan involves lots of running away, you'll want to go to the larger stage where running away is actually possible. If you plan on comboing your opponent left and right, Final Destination is a lot better than Battlefield. These differences may seem small, but they make a world of difference in tourney.
With that in mind, not every stage has to be this way. There are a lot of stages in Project M that come with quirky obstacles such as walls, moving cameras, and other crazy nonsense. These stages are a lot of fun to play on in a friendly environment, but these stages are not well designed for a competitive match with money on the line. This is why these stages are considered "casual" stages. They're still there if you want them, they're waiting on Page 2.
As for your suggestions, Pokemon Stadium 2 exists so you can play on the amazingly well designed Pokemon Stadium 1 without worrying about an unplayable rock formation or obnoxious tree getting in the way of fighting. Transformations are a lot of fun and part of why Pokemon Stadium was so unique and memorable in melee. However, in a tournament setting (or just really savvy casual play), some phases really interfered with the flow of the match, often leading to opponents waiting for a transformation to be over before continuing to fight. This really bores spectators (part of the reason Smash is so popular) and annoyed players, enough to ask for a Pokemon Stadium without worrying about a burnt tree slowing thing down. Thus, Pokemon Stadium 2.
As for replacing Dreamland 64 with Dreamland Melee, that won't happen. The melee stage could be included on Page 2 no problem, but Dreamland 64 is an important part of tournament play. This is a competitively minded mod, so DL64 is eternal.
