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Okay, first off, I think this is my first time posting in a Zelda related topic since I've been unbanned.
Second...uncomparable. Navi was less a character and more of a gameplay helper. Midna was far more for the story than lots of other crap in TP. If you must compare them, then fine, I'll choose Navi.
Why? Well, Navi helped you. The whole hey listen thing never bothered me. Nor did Midna's jibberish. Though I have to admit, if you do play either game for a loooooong while at once time, both things do get annoying.
Navi knew her stuff. OoT was my first Zelda game, and not to mention the first 3D game, so Navi was even good to veteran Zelda players and new players alike. With the 3D comes new stuff never in the 2D. Like Z targeting and stuff. That, let's face it, if you played either 3D or Zelda for the first time with OoT, you would've had a much rougher time without Navi. And a lot of what she taught held through in later games. Basically a 3D Zelda tutorial, and someone you could always count on.
Midna. Mmm. She was annoying in the beginning. After her change of heart after you-know-who (spoilers, whatever) dies, she is a lot better. But the whole relationship thing between the two can go rot in a sack. First of all, it happened when she was still an imp. Blech. And even when she returned back to her true form. It's like, they are both two seperate species, Hylian and Twili, if you played the game. To me, a human-like person loving an Imp is like beastiality. I liked the whole relationship between Link and Ilia a far lot more than Link and Midna. And as stated, the beginning, before her change of heart, she was just, to put it bluntly, a bee eye tee see aych. And she easily used Link. Excluding her first personality and the whole relationship thing, she was a good plotline character.
Not much else I can say.