Sure, custom moves proved to be a flawed idea. Can't exactly fault the community for trying. It was a fresh idea that helped out characters like Ganondorf and Palutena. It just made other characters like the Villager OP.
Custom moves were pretty cool. The problem wasn't in the balance. The major problem was in tournament setups. Not only did all the customs have to be unlocked to be fair, but the sets had to be pre-loaded. If there was an easy way to unlock all customs (like an affordable coin purchase, something all used Smash saves would have plenty of), plus the ability to pick each move (instead of a set) from character select, it could have worked out just fine.
The minor problem was, "This isn't Melee, so I don't like it." A vocal minority of the Smash community always objects to change, which is why you get so many quick no's to the question of metered Final Smashes. But the more considerate majority is the type that got the inclusion of "hazards off" in Ultimate, a suggestion that should add a lot more stage variety to competitive play.
I like the idea of Final Smashes. The problem before was that the Smash Ball was a terrible implementation for competitive play. Fun for parties, the Smash Ball often distracted from the actual fight, plus the RNG of which hit gets it, where the ball went, etc. Making it metered may change gameplay, but it's not RNG and it's not imbalanced towards characters with higher mobility. And if games start ending too fast, play with a higher stock count. And really, considering the probable buff to the edgeguard game (harder to sweetspot the ledge, further blast zones not as easy for every single character to recover from, no more 5x air dodge into invulnerable up+B), I can't imagine the game will be played with just 2 stocks anyway. It will likely be at least 3, but we'll have to see how the offense vs defense meta evolves as the game is learned after release.