I've never seen Ganondorf as plain, and yeah, I do think he's cliche, but I don't think that makes him a bad villain.
Very few of the Zelda games have ever made Ganon's motives very clear; that is something I'd like to see be explained more in future Zelda games. One of the few games I can think of that shines at least a little light on his whole reason for what he does is the Wind Waker. At the end of the game, Ganondorf says something to Link and Zelda that I think most people just overlook.
My country lay within a vast desert. When the sun rose into the sky, a burning wind punished my lands, searing the world. And when the moon climbed into the dark of night, a frigid gale pierced our homes. No matter when it came, the wind carried the same thing... Death. But the winds that blew across the green fields of Hyrule brought something other than suffering and ruin. I coveted that wind, I suppose.
I think this quote explains his motives in Ocarina of Time. Remember in Ocarina of Time, Ganondorf was king of the Gerudo? Well, the Gerudo people weren't bad people, right? So let's just say for a second that Ganondorf started out like them. Put yourself in his position. During the day, the heat was unbearable, and during the night the cold was unbearable. The game never says it directly, but the Gerudo were suffering in their land. So Ganondorf was the king of a people who were dying due to something he couldn't control: the wind. I'd like to think that he started out with somewhat good intentions. Maybe he was trying to take over Hyrule so that he could relocate the Gerudo to some place better? That doesn't justify attacking the Hylians, but that would have at least given him a reason. My guess is that once he got his hands on the Triforce of Power, he got out of control and just wanted to take the land for himself. What started out as a king who was genuinely concerned for his people turned into a man who was power hungry.
But what about the Wind Waker?
What did the King of Hyrule say?... That the gods sealed Hyrule away? And they left behind people who would one day awaken Hyrule? How ridiculous... So many pathetic creatures, scattered across a handful of islands, drifting on this sea like fallen leaves on a forgotten pool... What they can possibly hope to achieve? Don't you see? All of you... Your gods destroyed you!
Sooo, I think it's pretty obvious here that Ganondorf really didn't like the new Hyrule. To be honest, I can't say I blame him. I mean, practically 97% of what used to be there is covered in water. I think his motives from the end of OoT carry over to TWW, though. He's been sealed in the Sacred Realm for who knows how long, so he's clearly going to be angry. Then when he finally gets out, the land he pretty much had control of is gone, which only made him angrier. Ganondorf fully intended on bringing the old Hyrule back, but he either didn't realize that it would completely destroy people's way of life, or he just didn't care. I think it was the latter; he had become corrupt. He wanted power again, and he was willing to kill Link and Zelda to get it.
As for his motives in the other Zelda titles... I honestly don't know. It was pretty much the classic bad guy vs. good guy scenario, which was fine for the time. Nintendo's obviously been developing the stories in each game more and more. I'm hoping we'll get to see a more developed Ganondorf within the next few titles.
Well, that's just my two cents. I'm not a theoist or anything, so I'm sure I messed up a few things. Yay for onions. <3