She's not on this poll, she doesn't count.

Omochao isn't that bad in SA2 since you can attack him for fun.

I know, but he's still a shallow replacement for Tikal from Sonic Adventure, who, unlike Omochao, actually contributed to the plot.

I never found Navi annoying. Part of the nostalgia is hearing her voice :).

Of these two, Omochao. Navi is not even annoying at all. She is perfect and doesnt need to change.
Overall, Fi (TLOZ SS), Tatsu (XBCX) , Tidus (FFX) and the entire cast of FF13 are more annoying than both of them.

Especially Lightning, the Mary Sue bitch that somehow got her own spin off.

By my count Fi has the most votes via comments.  

Comments don't count towards anything not on the poll.

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.