My problems with custom loadouts are as follows:
1) They're clunky. Let's say I'm playing with 8-10 friends. Every time a new group of friends rotates in, we need to stop and spend a minute or two changing everybody's moves around? No thank you.
2) As the customization is apparently dependent on owning a 3DS version of the game, customizable movesets confer an unfair advantage upon players who own both the 3DS and the WiiU version.
3) Customizable movesets have too much potential to reduce the unique nature of each character's playstyle and are a balance nightmare, requiring the team to balance for variable combinations instead of one set moveset, an exponentially more difficult task.
4) Custom movesets create problems in-game, as you may not know what your opponent is capable of. If I'm fighting somebody who can switch around their special moves and they don't pull a particular one out until I am high percent, how can I guard against two or more moves which may well have contradictory properties?
I really hope Sakurai doesn't go for custom movesets, as it's just going to be a nightmare to implement in a way that doesn't end up being grossly unfair and causing tons of balance headaches.