So this is the video that got my rusty gears in my brain working about the whole ganondorf thing. I really recommend you watch it because it really gets you thinking.
The video is already above but if it's not showing then copy and paste the link and watch it.

http://youtu.be/RlqJZSk2GVY

Just copy and paste it :3 and watch the whole video. Like this guy has really good Zelda theories and I am convinced by them