Well, The Legend of Zelda is supposed to be like your classic fairy tale of heroes saving princesses and vanquishing evil. So, it does make sense that Ganondorf is sort of run-of-the-mill compared to say, Two-Face or Dr. Freeze from the Batman series.
That said, Wind Waker and Skyward Sword paints Ganondorf in more interesting lights. Wind Waker's Ganondorf is more the tragic villain fueled by jealousy of a prospering land while he watched as his people suffered in an unforgiving desert. The years of being locked up, immortality, and reflection makes him a different antagonist than the madman in Twilight Princess, the classic evil wizard in the original The Legend of Zelda, and the treacherous man in Ocarina of Time. This was a man, not a demon, consumed by jealousy, envy, and a desire for a better world. He still wanted power, but not for the sake of it or for revenge. That Ganondorf is my favorite despite that I didn't enjoy Wind Waker as much.
Skyward Sword revealed the origins of Ganondorf as hatred reincarnated. Following Demise's well, demise, he cursed Link's and Zelda's reincarnations with a hate that will follow them forever. Twilight Princess is the Ganondorf who seems to be the closest to Demise and some theorized that he survived not just by the Triforce of Power, but by Demise's - his own - dormant power. Wind Waker's Ganondorf's the furthest away from Demise, but due to the curse, that Ganondorf still cannot be his own man, but a spawn of hatred. Tragic and much more interesting.
Ganondorf lost even before he existed. He is bound by a demon's curse that will forever manipulate him.