I think the flak TP gets for having Ganondorf is a bit undeserved. Hyrule Castle and his different boss fights were fun in their own right, and Zant was still an interesting villain up until he was replaced.

Of course, it's not without it's flaws. Main issues I'd give it is that they do drop the ball with Zant once you finally face him. He goes from an imposing dark-usurper tyrant to a Ganondorf's goofy, whiny bitch-boy. While Ganondorf himself is kind of a non-entity, especially compared to Wind Waker which did a surprisingly good job at characterizing the guy.

Oops, All Ganondorf