This has literally never happened.
Oh? This happens all the time. It's not so blatantly put, but this is essentially why many changes are made. Bringing over Japanese players for OC3? Let's change our ruleset to be more like theirs. That's essentially saying, they don't like it our way but because they're high level/popular, we'll accommodate them (nevermind that there were only a handful of foreign players at the event).
Why were legit stages removed from early brawl touranments? Because ZSS and Olimar can't recover as well on those stages. That's not a legit ban reason. That's ... certain players who play ZSS and Olimar don't want to learn the stage or pick up another character for counter picks. So those stages were banned (from some tournaments for some period of time).
When you really think about it, all the decisions in a community are arbitrary. Some vote. Others have a small group that calls the shots. With smash, a lot of the high level players have too much influence on stuff like this. At least, this is how it was at specific points in this 10+ year history.
And when tournaments like Apex/MLG/Evo pick a ruleset, that pretty much cements those arbitrary values for a lot of other tournaments. The reasoning behind these rule sets and changes aren't so consistent.
I'm just worried because there are so many custom moves (Not just for Mii) and I get the feeling they're not gonna receive too much attention compared to the standard ones from the devs. Never know if we'll get one that's like the Mach Tornado and the Shuttle Loop had a baby that was blessed with the Holy Ghost of the Infinite Dimensional Cape glitch.
Then you're worried about balance in general not balance of custom moves. Whether a standard move, a custom move, a character, or stage doesn't get enough attention anything that slips through the "all seeing eye of balance" can cause problems.
Also the idea that people will want to play the 3DS version at tournaments over wireless with all that interference instead of playing the WiiU version is ridiculous.
If the TO doesn't make sure enough setups are available for everyone to comfortably play within the allocated time then the tournament is a bust and playing on the 3DS is not compensation, people would just straight up refuse and ask for their money back.
Welcome to the current state of smash locals. Some are great. Some are bust. But I'll tell you this... I've been to many locals that should have been a bust where the players just stick it out anyway.
So tell me, how many tournaments you know of where the players asked for their money back?