An overwhelming amount of the changes to customs post 1.04 have been a result of changes to the default moves (Ex: Fox's blaster, Ike's Quick Draw, Pikachu's Thunder Jolt, etc). Then for whatever reason, certain balance changes never carried over such as the added end lag to Shiek's needles and Villager's balloon fuel system.
Here's the thing about both Villager and Sonic. In the default meta, someone in the balancing team decided to nerf Sonic's spindash and Villager's Balloon Trip, but not nerf Hammer Spindash or Exploding Balloons. This lead to the custom variations going from being debatably equal to their vanilla counterparts (though I've always felt Exploding Balloons was better than Balloon Trip) to both of these moves being flat out better moves. They were balanced to fit the past meta of the game, but not the current meta, which is a huge problem. If we have to implement some sort of difficult to enforce rule on these moves, that is also a huge problem.
Community managers and TO's have the most power when it comes to these sort of things because of time restraints, what affects attendance, what hurts viewership, what's best for the health of the competitive scene, etc. Much of the time though, they have the community's best interests in mind. Customs became banned in NorCal and SoCal because of a community vote, not because the community leaders wanted them banned. Like Nanerz from NorCal is against customs, but if the community vote was the opposite of the actual outcome, I doubt him and other community leaders in NorCal would have placed a hard ban on customs.
While I agree, so many players are against the idea of any character have customizable specials that Mii's are probably screwed. The support for Mii's to be able to modify their specials among top players is weak compared to the amount of hate toward them and that's going to have a huge impact of their future. If a bunch of top players came together to purposely boycott any event that allowed for customizable Mii's, the future of Mii's are f'ed.