This may be off topic but one of the themes that kind of bothers me is the one team or the other trope.
For example, in OoT Ganondorf helps Ingo take over Lon Lon Ranch. It seems like Ganondorf would have better things to do than worry about a ranch, even a sizable one.
One thing I would like to see would be third party involvement. In my head, it goes one of two ways.
-Someone as powerful as Ganondorf (without the Triforce of Power) who is after it to make their own wish. Might make for an interesting new dimension to the games.
OR
-The gods get tired of the Triforce being used to wage wars or as an excuse for humans to fight each other so they send a lesser deity to strip the Triforce from Link, Zelda and Ganondorf and take it back to wherever the gods live. Part of the game would be to fight THAT character and release the Triforce back to either the Sacred Realm or to the previous holders.