This is a very difficult question for me to answer. Both of these two companions vie for my franchise favorite. While Midna was clearly the more developed of the two-scratch that-the most developed helper of the entire series, Navi emitted this special radiance about her that made you want to care for her. She seemed so innocent yet so dutiful and with Link unto the end. Personally, a ping went through my heart when she departed from the Temple of Time during Ocarina of Time's end credits. In the end, however, I believe Midna wins out for she played a major role in the story especially in relation to Zant and Ganondorf. Of course the cherry on top is the ending of Twilight Princess. Midna unleashed her true power against Ganondorf in a futile attempt to stop him. Also, the first time around, I believed she truly had perished when Ganondof emerged on his horse nearly unharmed with imp's helmet in hand. To top it all off, Midna's true form was extremely beautiful. No surprise therefore Link had a crush on her and fans have been clamoring for a return since 2006.
This is hard for me to decide but I think i prefer Midna.
In OoT Navi did a wonderful job of giving hints, enemy info and it was so cute when she asked 'Then do you want to talk to me?' if you said no to talking to Saria. I always said yes because she was just too cute. And also being so young at the time of playing it i was blown away that Navi talked, granted it was only three or four words but i still loved it, it humanised her and made her so friendly, at least for me.
While Midna didn't have any character information to give during battle, her powers really did help the game feel unique in wolf mode, transporting objects, jumping, and lifting very heavy things made TP feel more interactive to me than any other Zelda game before it, it was nice to have such power. Midna's story was also wonderful, it wasn't new to have your companion play a bigger part in the story we had already kind of had that with the King of Red Lions, but Midna's story was wonderful, and her small little nuances as the game progressed were subtle enough to mark a change in her personality without being blunt, replaying TP knowing what and who Midna is also brought a fresh and deeper level to the game which i loved. There were so many special moments with Midna too, such as running to visit Zelda with her near death on your back.
Midna is far less annoying and is a developing character in Twilight Princess and you get to follow her story. She's also like Zelda's counterpart because Midna is Twilight while Zelda is Light. I don't see how anyone can't like Midna. Navi is just boring and constantly pointing out the obvious about where you need to go and what to do.
Although Navi was very helpful when it came to defeating bosses and learning the names of enimies, Midna actually played a HUGE role in Twilight Princess. She helped you manuver and she talked to you during cutscenes, and a cocky personallity.
I picked Navi because honestly, he does have a personality, do you guys remember fighting Ganondorf, Navi couldn't take the evil, but he then comes back, saying he won't leave you again against Ganon. I was touched. That and also, Navi was much more help than Midna, 'nuff said.
Navi is waaaaaay more annoying, but Midna over-simplifies the game too much. As far as character depth goes, Navi was flat and boring. Midna had good character depth and a crapload of complexity. At the end of the respective games, Navi struck me as annoying and unchanged, and Midna was a lot less stuck-up and almost friendly. MIDNA ALL THE WAY!!!!
I would have to say Midna, simply because she was a supplement to the storyline.
Navi, on the other hand was flat out annoying. I watched a few walkthroughs of OoT for comparisons where the player would say, in the middle of his sentence, "my god, SHUT UP NAVI, you are Nintendo's single most annoying creation" and then continue his thought. Sure, she would change colors at certain times when you could Z-target or play your ocarina, but other than that I was like "yes, Navi, I know how to open a door >_>"
Midna was a little more useful. She provided the guidance for the jumping, turned you into a wolf, BROKE DOWN THE BARRIER AT HYRULE CASTLE, and wasn't overly obvious in her advice. *cough*Fi*cough* she added a lot of humor to the story too. When she talks about the monkeys in the forest temple, I was laughing pretty hard. She had attitude and sass, instead of being a flat personality. (A refreshing break from some of the personalities of Zelda throughout the games.) I say Midna
I can't decide between them. They both are good. I do think Navi is a little annoying because she constantly needs to talk to you, but I ignore it most of the time. She is very helpful because she gives you info about the foes you fight. I like being able to know the name of the enemy. I also like Z-targeting with her. I also like Midna because she has a huge role in the storyline. I like how she's ableto use the portals and warp all over Hyrule. The thing I don't like about her is what I said earlier about enemy info.