A proper response to this thread demands analyzing the advantages and disadvantages to each major partner including some you did not list in the poll options.
Navi
Advantages: Most nostalgia driven partner in series history. Seriously is there anyone who doesn't remember this female fairy. It's good Nintendo was successful in creating an exceptional first true partner in series history, enemy analysis, most faithful partner (Navi never abandons Link until his quest to save Hyrule is completed. ).
Disadvantages: Annoying as heck!
Tatl
Advantages: More developed and less annoying than Navi. Though Tatl was personally not nearly as dynamic and memorable as Navi, the fairy represented a huge step forward in terms of character development and set the stage for the King of Red Lions and Midna. Also, her name is an extremely nice pun.
Disadvantages: Very loosely connected to rest of series.
The King of Red Lions
Advantages: A helper who has an extremely intimate connection with the story. The King of Hyrule always was an extremely well-developed character whether as ship or boat. It was he and Ganondorf that made the story so moving.
Disadvantages: None.
Ezlo
Advantages: Very useful companion who cuts to the basics of what you need to know on your quest and briefly recaps the scenario each time you return to playing; also extremely hilarious.
Disdvantages: Occasionally annoying.
Midna
Advantages: Very fleshed out character who has strong relationship with villains in game, useful in dispensing information, a beautiful-and I mean beautiful-women at game's end! Midna was a template for all helpers after. Shame Fi disappointed...
Dsiadvantages: Annoying.
Linebeck (He's PH's sidekick not stupid Ciela

)
Advantages: A sidekick who displays an evil side. The fact that Linebeck can overcome his greed in order to assist you is a testament to his strength as a character. Nintendo should start leaning away from pure helpers more often.
Disadvantages: Cameo in Spirit Tracks is disappointing.
Zelda (Spirit Tracks)
Advantages: Appeals to contemporary teenage culture very much. The player can't help but feel embarrassed for Link when Zelda states at the beginning of the game, "Me...go with him?". Also, it's nice to see the damsel of distress take on a more prominent and center stage role once in awhile. Nintendo was wise once again. Very well played.
Disadvantages: Annoying shrieks when confronted by mice in Phantom form.
Fi
Advantages: Return of enemy analysis! Has arguably the best music theme in Zelda helper history! I can literally listen to Fi's them over and over again for hours! Ingenious, Koji Kondo. Also, Fi appeals to scientific minds and is a foil to Ghirahim but also a direct complement. Fi is to Link as Ghirahim is to Demise. Very well played on Nintendo's part.
Disadvantages: Annoying mechanical voice!
If only for nostalgia followed by character development I'd have to go with Navi followed by Midna in a close second.