As a Ganondorf main, personally I'd like to see most of Ganondorf's Brawl characteristics retained, with the following move / mechanic changes:
1. Longer Grab Range. Seriously, Ganondorf is 8 feet tall, and completely upright. His grab range should be among the best in the game just because of the length of his arms. Ganondorf's grabs are the best ways to keep people close so you can punish them with his much stronger regular attacks. I might prefer the Melee Down-throw because it was so very chain-able, but Gdorf's throws would work much better for him if he could actually *execute* them mechanically.
2. Warlock Punch -> Wizard Sphere. As cool as it always was to smash something with Warlock Punch, it's a terrible move overall and Ganondorf's Smashes and even tilt moves are more practical. How this would work is you'd press B to release it, and then your foe could only knock it back with a reflector or power shield. If you press Neutral B again just before it hits Ganondorf, Ganondorf sends it back, only now it's much faster and more powerful. Final twist: If you press B while its in mid-air and moving away from Ganondorf, it explodes like Zelda's Din's Fire. Limitation would be only one wizard sphere out at a time.
3. Bring back second jump recovery on Wizard's Foot. This would greatly improve Ganondorf's horizontal recovery game, and potentially make WF a nasty spike.
4. More powerful, single hit N-Air. The two kicks are terrible to manage with Ganondorf's weight. Just give him a single, powerful kick extention that can cancel out weaker multi-hit air attacks instead of this nigh-unworkable move.
5. Fix Ganoncide. Ganoncide should hold the foe beneath Ganondorf near full arm's length so they are KO'd first on the fall from an over-the pit Flame Choke.
Otherwise I absolutely loved Brawl's rendering of Ganondorf, especially the flame choke and the emphasis on power, with minor magical effects like the vacuum on the u-tilt. I feel with something more iconic for his B-move and some minor attack changes, Ganondorf can be a legitimate threat in his own right, and not be forced to hulk around the field chasing the opponent he just sent halfway across the arena with a single jab.
In general I like Ganondorf as a physical brawler because in the vast majority of Zelda games you're fighting Ganon, not Ganondorf. I always liked how Melee and Brawl emphasized him as a physical presence compared to the more magical triforce-suped up Ganon. Smash already had way too many sword users, so despite WW and TP (and arguably SS), I prefer the more brutish close combat Ganondorf.