I'm having a hard time picking between Midna and Fi. But after 10 minutes of thought, I found that I liked Midna better because of her strong personality and basically the fact that she can be pretty helpful sometimes.
I’ve loved all of the companions so far, actually (although I never played Minish Cap so I don’t know about Ezlo). Choosing a favorite is a pretty tough decision for me. Navi I liked a lot – she didn’t seem to have a ton of personality, but I felt close to her anyhow and she was pretty useful as far as enemy analysis goes. Tatl certainly had more personality, but her rudeness kind of annoyed me in the beginning, although I warmed up to her by the end. King of Red Lions and Ciela didn’t make as much of an impression on me, although I enjoyed them. Midna… she captivated me from her entrance all the way through to the end; she’s absolutely one of my top favorite Zelda characters in general. However, this is thinking in the sense of a COMPANION, and not just a general character, and in that sense I ultimately have to go with Fi as I really loved her in depth, to the point analyses. I feel she was the one that I got the most use out of. I can understand why some people found her annoying, but I personally didn’t. ♥
Navi and Tatl are my two favourites, probably because I play with them the most. I voted for Tatl though because of the two of them, she's the least annoying and grows to be more compassionate. Also I think Zelda from Spirit Tracks should be an option because I liked her guiding me too.
My favorite companion is definitely Fi. She may be emotionless, but the mysteriousness of her character and her purpose is great. She's the least annoying of all the companions, and at the same time the most helpful.
I, personally, like all of them (although the King of Red Lions is a bit iffy for some reason). Favorite's gotta go to Midna, because I love her character. She just sorta comes alive with all her rude and snappy remarks. Navi, like everyone says, is rather annoying with all her auto-tune sounding, "Hey! Listen!", but I'm kinda fond of her now. Tatl was like Midna, only on a lesser scale. Fi is my second favorite, simply because she's not a tsundere like Midna is, but she's like her own version of one. She's this rather emotionless robot-like being with artificial intelligence (I'm not too sure about that, I'm about halfway through the game! But I've read spoilers, of course -_____-) and in the end, shows some emotion. And of course that's rather heartwarming for me.
Midna is my favorite companion. Even though at times Midna gets too helpful, she was a great companion because of her personality, and more importantly, the plot surrounding her. We as the players do not realize who Midna is and why she is helping us until we find out later on that the game that she is actually the Twilight Princess and most of the plot is developed by helping her. Since I like deep and complex plots, I choose Midna.
Minda actually had a deep story that was a part of the game so it's hard to say you didn't like her the best; she's more then a simple companion. But you didn't add Zelda as a choice (Spirit Tracks); I had a lot of perverted fun with that at times. But I choose Navi here because I did like the undertones of importance she ended up playing in the game and MM; plus she's the first companion that comes to mind when asked this question - we love to hate her.