Customs I don't know about at this point. I was in favor of them at one point, but even though there wasn't much of the dreaded "custom jank" at EVO (with a few exceptions), they didn't make as much of a positive difference I would have expected either. Since the top players are pretty much all strongly against it, I doubt they'll ever be on by default, and I'm pretty much ambivalent at this point toward them (although Abadango's Fast Bike will be missed).
However, I see no reason Miis shouldn't be available in their fullest. In particular, there's no basis for 1111 Miis only, especially since Tournament Mode toggles them, always with specials intact, separately from customs, and all of the specials are unlocked from the start. In fact, in no mode with Miis playable (i.e. all but online With Anyone) does turning Customs Off remove Miis from the roster, or affect Miis in any way except removing their equipment, so clearly the specials are just part of the character. Mii bans are pretty arbitrary in general; the only thing I could understand being a decent compromise is sizes being set to Guest, and that's only if importing other Miis proved to be significantly more logistically complicated than making preset sets with Guest Miis (and I don't believe it is).