The Hero of Twilight was easily the most badass version of Link from his looks down to the vibe of his personality. When I got to Ganondorf at the end of OoT, I felt the tension of a decisive battle of good VS evil. In WW when Link faces Ganondorf, I felt a sense of urgency as this powerful full grown male goes toe to toe with an apparently adolescent Link.
With the Hero of Twilight however, I felt like he was the culmination of the Hero of Time's legacy. He was trained by the Hero of Time himself, has the best companion, was able to transform into a wolf, and he just felt badass overall. This time when I got to Ganondorf, I felt a feeling that made me say, "come at me bro!" as the battle commenced. To me, it was all about settling the score once and for all.