I'd like to rescind my vote for Navi, primarily because I remembered that Olivia exists, from this year's Paper Mario: The Origami King. Olivia is a delight, and Midna and her dumb single-anime-fang-smirk cannot hold a candle to Olivia's wide-eyed wonder.
Paimon is great. I'm still in the early stages but she could genuinely end up being a long-term favourite. Special shout-outs to Grimoire Weiss from NieR and Potato GLaDOS from Portal 2, though, which are close behind. Also do Palicoes count? They're pretty small.