Can you provide a source for all of those things you just listed? I know of a few things being changed with customs, but not much on a large scale.
ZSS I can't remember exactly, but I know everyone was talking about changes to her various customs when the first balance patch hit. I recall them being buffs, as her customs were useless when the game first came out.
Link's Power Arrow (I don't remember the exact name, but the "strong but slower" version of his Neutral B) was also changed in some way. I think it had something to do with the charge rate.
Rosalina had an exploit involving the Luma Guardian custom that greatly extended the length of her jumps. This was fixed with the first balance patch. A similar effect can be observed with one of the unfinished, glitchy customs Mewtwo has right now.
Palutena had the jump-cancelled momentum (not sure if that's the correct term) from Super Speed fixed.
Mii Brawler's "One Inch Punch", involving the Piston Punch custom, was removed in the most recent patch.
Sonic's Burning Spin Dash custom used to have some degree of invincibility frames that made it useful against projectile users. That's gone now with the latest patch, and the move is considered pretty much unviable.
The jump on Kirby's Hammer Bash custom was boosted in the latest patch.
Some of these are documented on Smash Wiki and some can be found in the character boards on these forums, though some are undocumented for some reason. The Luma Guardian High Jump fix isn't documented, but I can vouch for it as Rosalina is my main, and others in the Rosalina boards probably do remember it, as we did discuss it.