Hmm, there is so many good characters, but I'd have to go with Medli from the Wind Waker and Midna- either forms.
Medli was such a great character, she was very caring for Komali, but was able to focus very well on her true purposes. She was a very kind-hearted character, and being a sage, brought even more purpose to her. She was a very likable character. ^^
As for Midna, I'd love to see some Twilight Princess prequel or sequel, that would be very interesting. Midna was a very mysterious type of character to me, for throughout Twilight Princess, she often kept secrets and avoided talking about herself. Mysterious characters are a very good way to hook people in, for you are wanting to learn more, and you continue playing the game. This is what happened to me, so I found Midna a very good character, despite the first two temples with her, where I found her really annoying.
So I'd love to see these two characters return sometime in the series.