The more I think about it, the more I think custom moves have the potential the be the next big divisive thing. Like people who play items vs people who play no items. It'll be the purists vs the customs.
That is, unless, it is a huge pain in the butt to swap custom moves between fights.
If competitive community loved the heck out of the changed movesets from Project M, I'm sure the community can find a way to make an acceptable decision regarding the use of custom movesets. It will just help the game get a more balanced approach IMO.