The difference is that those aren't nearly as popular and played as Project M. Giving the option to set mains for every mod out there would be stupid. If we can set a main for a mod in the profile, there is no reason for not set mains for the 3DS and Wii U versions. The games will be different, different coding, stages and controls = different games. First, certain tricks you can perform in Melee (for example) are only possible because of the coding of the game, which mean there could be tricks or even glitches only possible to perform in one of the two versions of the game. As for stages, it is not a secret that tiers in Smash depend on which stages a game have, so the two games might have different tier lists. The controls are a really minor thing, but it still is a difference between Smash 3DS and Smash Wii U.
I really don't get this "Smash 3DS and Smash Wii U" are the same game mentality. They aren't! They are being developed mutually, but they have similar gameplay and mechanics, but they are still different games, even with different names (even Sakurai consider them different games, since he calls Smash 3DS "Smash 4" and Smash Wii U "Smash 5").
Anyways, this is my opinion in the subject, in the end it is up for the admins and mods to decide. I just don't understand why there are people AGAINST my suggestion. If you are going to main the same character in both versions, just put the same character in the boxes for the 3DS and Wii U mains.