I think Navi was more annoying than Fi first but it changed now. Fi is so annoying because she always have to point out the obvious and pop out at the worst possible moment every time. It just gets so boring.
My favourite Zelda enemy is Darknuts. Especially from Twilight Princess. I like how you had to destroy their armor first and and then defeat him while you're dodging his sword. I used the back slice and the great spin a lot on them :)