Twilight Princess.
The story was more dark and real, which made the characters stand out more to me.
Zelda wasn't helpless, she could fend for herself but fell defending her castle. Link being the avatar actually got more stand alone character development and t'word the end kind of went a little crazy. This stood out way more then in WindWaker or MM, where it doesn't really give much to who Link, The Hero of Time is other then the basic key plot points.
Now Ganon, he was depicted the best in this game, he looked somewhat real and really pissed off because of what he's gone through with the Sages, being trapped in the Twilight, Link and Zelda.
Here's the only thing I didn't like about this game. The sages weren't the same from OoT, spending the whole game explaining who they are not to use them in other Zelda games makes no sense to me (HS?), This Imho would have made the feeling of this game more like what they were shooting for the adult Link part of OoT and not that of a non-bloody DmC or Darksiders.