Just out of curiocity, I took a look at the moves Ganondorf still shares with Captain Falcon (bold indicates that it's a completely different move that is heavily inspired by the old one):
14 out of 24 moves (not counting getup attacks) is actually quite a lot (58%). If we say we don't care about the grab and throws, that brings it down to 10/14, which is 71%. Given that these two characters aren't related I can see why people are upset here.
As for decloning him further goes, his throws are the easiest thing to change, as all that entails is changing the animations. In fact, his forward and up throws already have different animations, and I was hesitant to count them, but they do have the same concept as the originals, so you'll probably have to get a tad more creative here.
But throw animations are mostly just fluff, and there's only so many ways you can throw someone anyway so a lot of characters will share certain concepts. His aerials and specials are the more impactful ones to change. For his aerials, neutral aerial is one of Ganondorf's best moves, and changing it makes him feel worse to play (as seen in SSF2) so that needs to stay. Down aerial is a fan favorite move in the roster, and should stay as well. Up and back aerials are kind of difficult to conecptualize, so that's probably why they've stayed the same, but there's no real reason why they can't change. For a conservative example, instead of backfisting for his back aerial, he could torque himself in the other direction and deliver a palm strike.
The specials are probably the biggest thing that fans look for when determining a character's clone status, so I'd say these need the most consideration. Unfortunately, the specials are all iconic, and kinda have to stick around in some form. Except for Dark Dive. It was never a strong concept for Ganondorf, and if nothing else, should be replaced with a simmilar move that isn't a command grab. If Ganondorf isn't given a reflector, I think Wizard's Foot really should be altered to allow him get around and/or through projectiles more easily. Warlock Punch staying is probably a hot take here, but I think it should be given added utility, that can be accessed by not going through with the full punch. Maybe make it like Failnaught where the move has a baseline functionality, but allows you to commit to the dummy strong casual option if you want to. Or just say "screw it" and make it a reflector and/or counter and watch the world burn.
The point to this that I probably didn't properly convey is that there's still some room to declone Ganondorf, and while I don't know how they'll go about that, a full rework isn't required; just substantial tweaks. When it comes to his special moves, a lot of these tweaks could be justified entirely on the basis of making him more functional as a character. lol