Yeah, I know. Just pointing it out to future people who might post here and get confused...then we have to Gannon-Ban them ;)
Hmm forgot about them. I didn't really like Thunderbird, but Shadow Link was cool.
First of all...Ganon and Ganondorf are the same person. Secondly, you can't count Aghnaim as the main antagonist of ALttP, because Ganon(dorf) was. Same thing for Zant in TP...
Aside from Ganon(dorf), I'm gonna say Vaati. Bellum was pretty...dumb.