What can I say, I am a sucker for the 2D Zeldas, but once they get into the later series it is not as cut and dry.
The 3D Zeldas all have their distinct styles and advantages and disadvantages. For instance OoT is probably the most cherished for being the first 3D Zelda and the game everyone looks to as the standard, but is that standard the best? In many things yes, it is...but in others no, it fell short.
Majora's Mask is the most different with a unique story and environment and atmosphere. Its a great game, but also one of the least Zelda feeling in some people's opinions.
Wind Waker is perhaps the most controversial Zelda game. The graphics, the ocean, the lack of ground exploring for a sea adventure....it is all very different. Add to it a rushed feel with a dungeon or 2 missing...but then again everything above that is a fault can also be a strength...and it is also one of the more memorable Zeldas...specially the fantastic end battle.
Twilight Princess: The game that appeared to do everything right in giving fans what they wanted in coming back to OoT tradition, but then became too familiar to the original. Great Wii controls, big vast world, a good number of dungeons and adding even more story elements with triggered story events to play through....but then there are the wolf segments some people hated. And, they still basically visited the same story of a dark and light world for the 3rd time.
I think the 3D games are doing better for bronze because most Zelda fans believe and LttP is the defining moment in the Zelda franchise that set the course of the series for the future...and is one of the most careful and finest made games of all time. Many people vote it, for best because of just how much influence it has on the entire series...and how good it is.
Once people already voted for LttP it opened them up to vote for the 3D games. I honestly don't know why Link's Awakening is getting the same number of votes. It is a great game, and the characters within the game world are more fleshed out and interesting than the characters from LttP, but to me it just feels like I am carrying around a portable LttP, which is cool...but still pushes the nod to LttP, as the better game.
I really, can't vote for the 3D games because I don't know which of those is better, or which I want to play again...but I know given a chance I would play LttP again...at least 2-3 more times. And I would play a remake of Link's Awakening again, but probably not the original or DX version.