Well, technically, Ganondorf died. Link kills him at the top of the fortress in Ocarina of Time...
But he had the Triforce of Power, which apparently grants the user some sort of immortality because he came back to life as Ganon. It seems that he took on the shape of Ganon because that is what was in his heart (like remember in LttP, people in the game tell you that if you go to the dark world without a moon pearl you will turn into whatever is in your heart....Link turns into a pink bunny...). Remember at the end of Ocarina of Time Link and Zelda couldn't kill Ganon....at the very end Link impales the Master Sword straight into Ganon's brain...but Ganon still doesn't die, and the Sages have to imprison him to the Golden realm.
Now, WW takes place a couple of centuries later right? Ganon breaks out of the golden realm...but he's now back to his Gerudo self. Obviously this is not explained, but I think the solution is obvious. He can use the Triforce of Power to turn back to his human self. I mean, it should be possible right? The Triforce of Power is a powerful magic artifact...it is the embodiment of the power of a goddess. So I think it's fair to assume that it can easily turn Ganon into Ganondorf and vice versa.
EDIT: Oh yeah, and Ganon did revert back to human form right when he was being banished...I think he did that voluntarily so he could curse Link and his descendents. I still think that his precious allows him the change back and forth at will....or maybe under certain conditions. Besides, Zelda can use her Triforce to change into sheik (who was a male in Ocarina of Time...but for some reason a boobless female in Smash Bros...In the smash bros melee manual it calls sheik a she, and also in the trophy screens...and shieks voice sounds like a girl trying to be a guy...but if you look at sheik's model it looks like a sort of skinny but muscular guy...but without boobs....but then again also without that other thing that guys have... o_O ...anyway in OoT i personally think it's quite obvious that Shiek is a male, even though he still has some traces of feminity like zelda's eyes...although you wouldn't know unless you knew that was Zelda...) So anyway....
Now, enough bickering about the pointless story things...Lets talk about what makes Zelda great, the gameplay.
And since we are on the topic of triumph forks, lets start with that. We already know that Ganon(dorf) can use the triforce of power for all sorts of misdeeds like calling a dark army to his control and using dark magic and fun stuff like that. And Zelda and Shiek can obviously make good use of the Triforce of Wisdom...Zelda uses it to turn into Shiek, and magically open doors, and hold down Ganon so link can slice him up...not to mention all that Smash Bros. magic.
But what about link and his triforce? Why doesn't he get any special powers??? You could say it gives him super strength because well, by the time you have lots of hearts you can basically take a dozen times more damage that any other human. But still....I think link needs to develop some triforce powers in the next game. Maybe they could be magic powers...(like the medallions in LttP and the crystals in OoT)...or they could be instrinsic powers...like the force abilities in the Jedi Knight games...temporary super speed to deal with a roomful of enemies or something...I'm sure they could think of much more original powers.
Also, they need more moves in this game...more like the swordfighting movesets in Soul Calibur, not just the standard left slash, right slash, stab, and chop, of OoT/MM/WW.
Also it would be nice to be able to get some weapons that aren't swords. Maybe a spear? Throw it at an enemy and impale him, then finish everyone else off with dual daggers, then go pick up your spear again...Actually this is already in WW, but it's all clunky and unrefined. In the new game you should be able to pick up an enemy weapon and use it just like your own (not just the 2 moves from wind waker: attack and thrown). You should also be able to jump attack and parry with them... these moves use the A button but in WW pressing a would throw the weapon. Pressing R would drop it, disabling blocking (with either your shield or the weapon itself). They should make dropping and throwing done by, say, holding R and then pressing A...