I prefer Midna. She was actually part of the game. Navi, though actually told you about enemies. Navi is better for newbs in Zelda, but Midna is better for others.
I've played TP, but I prefer Navi over Midna. Midna and Navi could both teleport, but you could play the Ocarina and talk to Saria with Navi! :D Also, Navi could show you a "secret" area (somewhere that you'd have to play the Ocarina or use the Megaton Hammer) from a distance, whilst Midna was stuck on your back.