Jr, Diddy, Falco, Greninja, Mac, ROB, and Zelda all have valid selectable sidegrades.
Sakurai himself could have given any given custom to a character as default (see: Boomerang) and it quite possibly would have resulted in a slightly different meta from what we have now. The meta, and by extension, character strengths, vary by ruleset, and as such, trying to compare winners and losers across customs or not is comparing apples and oranges.
And the more I use it, the more I actually like default Dr Tornado for anything short of hard offstage reads. Lots of Rosalinas prefer default Luma Shot since it doesn't have a massive midrange blindspot. Dashing Assault is a recovery variant that loses all actual aggressive value/shield breaking potential Shield Breaker is good for. Iai Counter is generally better but can lead to some Little Mac offstage counter situations that put you in a worse spot, and Crescent Slash makes your nearstage game riskier due to its lost vertical. Mario has versatile fireballs (unlike Doc's EVO sets, Mario's include both, and honestly all three should probably be present at least once), very selectable capes (discussed in detail in the actual EVO moveset page), and can trade recovery for a comboable kill move instead. Link at least generally wants his old Boomerang, and can trade recovery for an extra meteor via meteor bomb. Tink has some similarly valid tradeoffs on bombs, up special, and bow. Dorf is essentially set in Dropkick and Dark Fists, the other two are versatile by preference (since none of his B moves will really ever hit and all three sides have valid pros and cons). Palutena essentially always has Lightweight and Superspeed because they're that good, but the other two have full range of options bar the laughably bad Heavenly Light.
So, regardless of the current state of the custom moveset project, which is suitably under review, there's quite a bit of valid variety that I, personally, am sure would shine forth if they weren't such a deliberate nightmare to set up. If it was as simple as choosing a special for each direction (like choosing an assist for each character in Marvel), I would bet money we'd see wider use of more interesting things.
Either way, I must agree and emphasize that the presence of choices, even in the presence of "clearly superior" choices, leads to better metagame growth. If it didn't, all Smash games would have banned down to their top tier character on that character's most interesting stage long ago. Thank goodness we haven't.
Also, normal Shoryu is better when you can't afford the time/thought to do the input. i.e. while recovering without threat from the enemy. Even if you consider that just "poor Ryu play", there still exist choices in which strength of Shoryuken (and all other moves) to use.
Simply put, some things will have objective superiority. But unless you allow the others, you can literally never know. It's like eating pizza from one restaurant once in your life and declaring that there is no other good pizza and all other pizza is time consuming jank.