I think a lot of us are victims of the over-hype of TP. We waited so long, and the game became so built-up, that when we finally got to play it we couldn't help but be disappointed. This is also because what Twilight Princess did well, it did SO well that other things that were only done "acceptably" begin to tarnish in comparison.
No, TP isn't perfect. But neither is OOT.
This brings up an interesting point: barriers to immersion. It's hard to go back to play Ocarina of Time for someone who's already played Wind Waker or Twilight Princess because of these increased barriers to immersion inherent with an older game. As I see it, there are two main things standing in the way of a gamer and the game communing: presentation (graphics/sound) and control.
As presentation gets better and controllers are refined, it becomes virtually impossible to step back to a more primitive time and enjoy a game in its original context (as gamers experienced it when it was first released). How does the saying go? "A mind once stretched by a new idea never regains its original dimension" (Oliver Holmes)... in essence, we are creatures of the present whose values and predilections are shaped by what we have experienced. Further, as nostalgia begins to take a role in our evaluations of games from the past, these evaluations become further divided from those who experienced it much later, out of its historical order.
I would also argue that, as we age, we become harsher critics in everything, games included. Yet, we retain our original judgments of games from when we first played them, whether that was yesterday or as a seven-year-old. What I'm trying to get at is...
No game is perfect – even the game you look back on with the fondest memories. You were just more accepting then, and more critical now. How can one judge two games from different eras, and played by (in essence) different people, side-by-side?