When Melee came out, all Ganondorf had done prior to that was be mentioned in the instruction manual for LttP, play an organ, fire a beam of darkness (which Melee Warlock Punch gets its voice clip from) and shoot orbs.
It wasn't until Wind Waker that Ganondorf became a badass with swords. Where he's flipping around and flowing with two large swords. I really like this Ganondorf, but his style is also somewhat specific of his "Toon" design.
Then with Twilight Princess he somewhat adopted more of a Smash style, with more brutal, powerful motions to his attacks. He also gets his forward tilt, down tilt and side special (all added in Brawl) from Twilight Princess. So his improvements since Melee were adopted into his moveset.
Is there really a need for him to get a total redo if the redo would more or less be full of made up Smash original moves anyway? Especially considering his side special isn't going anywhere.
The only improvement I think they could make would be to give Ganondorf some orbs that he fires with throws (like Mewtwo), give him some kind of unique up special because that move is still very much Falcon's, and make sure he has 100% unique normals. Keep Warlock Punch, Choke and Wizard's Foot.