As for the last poll - I'm surprised that Wind Waker beat Twilight Princess so badly. They're both top-shelf games, but WW was very controversial. While TP has its haters, it never had the bad press that WW had. Just surprised. I assume TP will probably take 6th, but, while I did enjoy the game, it just doesn't beat FSA for me.
My problem with Twilight Princess is that it's fractured development led to a very mismatched final product that, while still good, never really comes together. You have a very definite first half and a very definite second half, and the two halves are radically different in storytelling and tone. There's also the Twilight Dimension and Link's wolf form, which both come off as wasted and arbitrary since the game doesn't really
do anything interesting with either one. Toss in dungeons which emphasize the new Zelda law of "this item shall be used in this dungeon heavily, but will
only be used in this dungeon"; an underwhelming selection of weapons; and kind of an underwhelming cast of characters (outside of Midna), and it's just an "ok" Zelda game. Of all the Zelda games, it's the one that's hurt most by the stagnant Zelda formula.
Wind Waker has some severe problems, but it more or less tries to take its central conceit of the ocean world and just run with it.
As for this next round, I'm probably going to have to go with either the Oracle games or Four Swords Adventures. Haven't made up my mind yet.