I feel like custom moves take away from the actual game for various reasons...
1) Potential Exploits - Sure 'some people' claim that all potential exploits are believed to be discovered, but with as much content as Nintendo put into Sm4sh, I highly doubt anyone's capable of being confident in being 100% positive in this. Not that all exploits are bad, but tournament play isn't where we want this to be recognized either.
2) Aren't custom moves separate from game console to game console? They're unlockables. I haven't messed around with them much because I've just been playing other modes and neglecting the whole customs completely so feel free to correct me and elaborate, I'm still learning the whole custom changes, but what if one console has a custom move that another doesn't? In live tournament play we'd have to wait for a specific console to free up and in online play it gives player advantages of who has access to what.
3) Are special moves separate from custom settings? Not sure where the line is drawn, but this poses more problems just for sake of natural character play - though, I don't think anyone has to worry about this because I think it may be a completely different thing, again correct me where I lack the experience. lol.