Neanderthal
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Hah! Would love if they made a Zelda different and intriguing like that. Like the pulp fiction of Zelda gamesHeh- well, I still agree with what you said before you edited it. Have the heroes have their arc versus the villains, have the villains group up together to fight some greater villain or something separately from the heroes... I know that the Smash Bros. versions of the characters aren't cannon or even necessarily the same characters, but it definitely helps to have them at least seem motivated in the same way as their cannon counterparts.
In terms of Ganondorf being playable in an actual Zelda game, I wouldn't mind a game that made you play through a story with Link, Zelda, and Ganondorf where they each achieve their fated destiny for that generation.
Ganondorf's story would have him ousting power from another evil lord.
Zelda's story would involve her trying to figure out what is going on with the kingdom and searching for the destined warrior. Could focus more on magical stealth and espionage than the other segments.
Link is found by Zelda and learns how to defeat Ganondorf and the other evil lord.
All essential parts for destiny, you could even play as Ganondorf capturing Zelda! Woo!
Yeah I don't think he would necessarily need to be a good guy or teaming with Link to be playable. I see him as being too evil and prideful to team with Link or Zelda.
Definitely could use some shaking up as the forumla of Zelda is getting a little predictable.
i.e. Zelda getting taken away, a new bad guy messing with you for the whole game and then shock! surprise! Ganondorf (/Demise) turns out to be the real bad guy behind the scenes all along.