Sorry to chime in such a heated discussion with little posting credential, but, has there been any talks of what each character's optimal moveset is or is likely to be? I think it'd play a big part of digging deeper into what customs add to the game.
With 58 characters in the game and a lot of character's sets being preference-based that's pretty hard to do unfortunately. The custom moveset project linked in the OP has the 10(?) generally agreed best sets for each character though. It's been a while since I've experimented with customs unfortunately, but I'll give my brief thoughts for characters I play.
Greninja
(1111/2111/3111) - Greninja's shuriken startup lag had been buffed since doing the original custom moveset project and heavy shuriken usage and camping has developed to become an important part of some Greninja matchups, so default is likely still the optimal set. However, the kill confirms that the other 2 shurikens provide are incredibly useful in matchups where either traditional Shuriken usage isn't as crucial or vs characters that are traditionally difficult to kill. Stagnant Shuriken's ledge pressure can also help for characters whose ledge options don't deal with that well. Down B 2 (the explosion) can be argued over Substitute, but both are rather niche moves. Substitute can help in certain matchups for edgeguarding or alleviating projectile pressure. Both Side Bs and Up Bs are outclassed by defaults.
Charizard
(1311/1331/1313/1333) - Dragon Rush is Charizard's best custom, granting him a great burst option, recovery, and edgeguarding tool. The other side Bs have their merits with their super armor and raw power respectively, but Dragon Rush is probably the option that grants Charizard the most viability. Flamethrower has become a near necessity in some Zard MUs like Cloud and Diddy for its edgeguarding and ledge pressure and ability to destroy certain projectiles and items, so I don't think the other neutral Bs have enough to offer over it for the most part. Fly High allowing Charizard to go deeper for edgeguards and survive longer is pretty big, though Fly's super armor helps a ton both offensively and defensively. I honestly forget the merits of Rock Hurl over Rock Smash, but I remember it being pretty good, so I added sets with it for now.
Zelda
(131x/121x) - The Din's Fire customs make the biggest difference with Zelda probably. Din's Blaze's ability to set up traps at the ledge and especially offstage is so good, so I think it's the best. Din 2's relatively low startup on the other hand gives it some merit. All the Phantoms are about equally good imo and have their own merits, so the last slot is left as random.
Sheik
(2211/1211) - While Paralyzing Needles and the Bouncing Fish customs are quite good (Pisces is a favorite of mine), the other two needles, Grenade 2, and regular Bouncing Fish provide the most optimal options. The speed of Needle Storm and Piercing Needles are needles, with the former having the advantage of damage and the latter shield pressure. Bouncing Fish is incredibly versatile, granting and excellent edgeguarding tool, confirms into it for killing from a variety of moves, and excellent recovery. Grenade 2 is useful simply for its confirm into U-smash and other kill moves at higher percents, I believe it outclasses the others solely for this reason.