Omochao.

That thing has no real purpose.

I voted for Navi. I would've said Fi but Skyward Sword HD made her MUCH less annoying

I never found either of these annoying. Their roles lasted less than ten seconds in games that were several hours long...

What did the HD version do different?

All of Fi’s advice is now optional. So she won’t jump out to remind you of the thing you JUST learned lol. She’s just much less of a nuisance. 

I came in here to say fi as well. I don’t know the chao but looks like it’s from sonic adventure 

Fi wins this poll.

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

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.

By my count Fi has the most votes via comments.