The only thing I can see getting changed with Ganondorf is a few of his specials. He might get dead man's volley (down-b replaces wizards foot), His up-b may get replaced by something else as well (Some kind of levitation, some kind of teleport? Just spitballing.) and maybe some stuff with a sword for his tilts. He's actually very differentiated from Falcon, all he really needs are some status changes and stat improvements and then hes all good. Oh ya, get rid of that up-tilt, its pretty garbage and impossible to land (harder than warlock punch)
I doubt they need to replace him with toon Ganondorf, the alt costume thing could work. Im not really sure on his body proportions, but I could see it i suppose.
He hasn't been revealed yet for a very good reason, which I believe hes getting some kind of rework to his moveset or abilities. He's one of the highest priorities to get reworked a little bit, IMO, along with Falco a little bit more (mainly just his specials as well.)