Never minded Navi. It was Tingle that drove me nuts. Navi was my little buddy. I liked her (it?).

I do agree that having it integrated into the plot like that is preferable.

I don't think anything can compare to this monstrosity...

I could somewhat bear the night time stages of Unleashed, but this "thing" was a constant annoyance any time he showed up.

I really liked Navi the first time I played Ocarina (I was around 13 at the time), so she has the nostalgia factor going for her. That said, she is extremely annoying. But not nearly as bad as Fi, fuck that piece of shit, nearly ruined the game for me.

I didn't play Sonic Adventure so I'll have to go with Navi between the two. That being said Slippy from Star Fox 64 was one of my most annoying side helper character.  Edit now that I think about it Morgana is the answer from Persona 5.  He had a big role but had similar moments when he offers advice, aren't you tired stay in your room tonight.