I don't really know, nor care, who the main villain is, as long as it's done right. By that, I mean he/she/it has a place in the plot, is not tacked-on, and fits with the general theme of the game. I don't want another
TP where Zant was made out to be really cool and a good villain (if you know what I mean there), and then turned out to be a wimp who was nothing without his "god", Ganondorf. I want a real villain! One who fights honestly, does not depend upon another, and who is genuinely awesome!
Most Zelda games I've played seemed to have this:
OoT,
MM,
TWW,
PH, etc. Then that changed with
TP. Huge disappointment for me, as well as others. Nintendo could have done a lot with Zant, but chose not to. Why? Maybe they thought the fans wanted Ganondorf? Maybe they thought the game wouldn't be the same without him? Whatever their reason, it wasn't a good one.
The fact of the matter is that Nintendo ruined a perfectly good new villain with
TP, and I sure hope they don't go there again with the new Zelda Wii.