I can definitely see where you are coming from. I understand that notion.
It seems like the 3DS has very few legal stages, but the Wii U version seems to have many more legal stages. Maybe the separation could be done in the Wii U but not in the 3DS? I feel that even though both are flat stages, the differences in underbellies and length (possibly blastzones but no one has tested it yet) make them different enough in my opinion where certain characters will excel much more at one of the 2 types of FD over the other. I guess we'll have to see how the meta and stage list evolve later on.
At the risk of veering off topic, I don't really understand why everyone says we have next to no legal stages, and if I'm being honest I don't really like that it's happening at all considering a) the game is less than two weeks old, b) a very small minority of us actually have the game to test any questions with, and c) most of our knowledge of the game comes from streams which are mostly either doing For Glory matches or just not playing anything other than Battlefield/FD/Omega. In other words, we know
very little about a lot of the stages and I don't like how a lot of them are getting written off based on what I see as preconceived notions and hearsay. (Case in point: In the Paper Mario stage discussion thread, the OP requested video footage of the Blooper in the second transformation, since apparently it was incredibly disruptive. However, an actual ingame tip explicitly states it does not attack but merely makes waves that rock the boat you fight on, which is borne out by a stream I happened to be watching a day or two prior on that stage. This tells me that other stage "knowledge" is also suspect and deserves a thorough, honest experimentation and review stage.)
More on topic, I believe FD and Omega stages should all be grouped together under one heading for the sake of stage striking and DSR. In game 1, it's probably best if only the real FD is allowed just for simplicity's sake, but for counterpicks I think it should be up to the player who picks FD to possibly pick an Omega stage in its place. Although the under-stage geometry may be different between Omegas, I do not feel it impacts the match enough to warrant multiple copies of what is in all other respects the exact same stage. It would give characters that do well on FD an unfair advantage in the stage selection process that could only be overcome by additional stage strikes, in which case why not do away with the middleman and just lump them all together to begin with.