As far as companions in 3D Zelda games, Midna ranks as the top. Not only does she offer significant help in many aspects of gameplay (including transformations, multiple targeting, and teleportation) she also grows as a character.
Navi was never annoying guys. She said "hey", "listen", or "watch out" maybe once evey hour or two. This Navi is annoying shit has gone on too long.
Something must've been 'right' with your copy then. Or they reduced the occurance on the 3ds ver. Idk, but for sure on the N64 ver. it was more like "Hey!" "Listen" "Hello!?" Every. Few. Minutes.
I for one applaud Midna (as well as the artist) for this.