Ganondorf is the holder of the Triforce of Power how can you say he isnt a main character of the series?
With the timeline, I decided to study if Ganondorf really is the main character or not. What I gathered is that it's not because he's the holder of the Triforce of Power. It's because he's the ultimate villain. In FSA, Ganondorf is even reincarnated and controls Vaati. This game is the connection of the Four Sword Trilogy with the Triforce Saga.
Interesting though, Ganondorf really isn't present in half of the games. To note:
Skyward Sword - Ganondorf's past life
Link's Awakening - OoX direct sequel
Majora's Mask - OoT direct sequel
Phantom Hourglass - TWW direct sequel
The Minish Cap and Four Swords - Vaati
Spirit Tracks - Malladus
I could divide the timeline into three: The Triforce Saga, The Four Sword Trilogy and New Hyrule. Ganondorf is the main antagonist of the Triforce Saga, Vaati is the main antagonist of the Four Sword Trilogy (but is overruled by Ganondorf) and Malladus is the main antagonist of New Hyrule.
OK, so overall, Ganondorf is the main antagonist. My bad. :-P