Besides the main three, mine would probably be between a few.
I've always liked Darunia because of his Goron personality among other things. (The epic dance)
Rauru and his many re-incarnations are also some of my favorites due to his/their wise characteristics.
I also liked Ilia quite a lot. I always thought her and Link had a lot of chemistry and similar characteristics.
A lot of characters to choose from, Pry first is Dark Link, i wish TP or SS would have had a fight with him. Other than that it would be definitely Past Impa from SS, such agility, and power! Where is the side quest to play as her? Her short battle with Ghirahim at the Temple in the desert, she shown potential, Legend of Impa!! jk
Tough decision, I cant pick one so it would have to be Makar and Skull Kid. Two solid characters in their own right, I really liked Makar's story in the Wind Waker, and Skull Kid is just so intriguing and awesome.