Triforce, I think it was the horrible gameplay/environment segregation that ruined the games. You have this really limited means of traversal for the player and everyone else, yet you are the only one seen using it. Sure, you didn't see travelers in the other games, but its a huge wide field in most cases, you can assume that they're just out of sight. In ST and SS? Nope, it just doesn't work.Anyway, love the series to death. Grew up with the games, and I'm probably going to play them until the last one.
Personally, my favorite has to be TP. People are far too quick to judge this game. The structure might be similar to OoT, but the story is far from the same. Zelda never really needs saving, the companion is the real star with the hero being their tool, and the plot mcguffins are far more interesting. While the Master Sword does pop up in the middle after three dungeons, its only out of neccessity and not because of your goal for the first act. And unlike OoT, you go on the second act quest not to gain access to Hyrule Castle, but to gain access to the cause of everything. Hyrule Castle, much like the Master Sword were consequential events, and not direct effects of your actions. Its much better then what LttP and OoT did in terms of story, much like SS.
Speaking of LttP, I think TP is more like it then OoT. Sure, OoT follows the same plot, but the parallels are more apparent in TP. Saving a princess from the sewer prisons, Usuper/Wizard being controlled by Ganon, forest location for the MS, its all very similar.
As for SS, the game easily comes after MM for me. Interesting characters, excellent plot(the 3 act structure was amazing, don't tell me it wasn't), and the overall effect the game has on the series is enough for me to hold it in such a spot. Those final hours from the final dungeon, to the last shot of the game are easily the best final hours in the series. However, like T89 said, its missing something. Which may/may not be what I opened this post with.
I do not want to go through a list war, but my rankings have to be:
2D Zelda's
OoS/OoA
MC
LttP
LA
ALBW
ST
PH
Z1=Z2
3D Zelda's
TP
MM
SS
OoT=WW