I don't like either of them.
I'm not much of a shipper in the first place, but the Wind Waker has one of the most obvious cases of Zelink in the series, and for me, also one of the more likeable incarnations of Zelda for me to get behind that ship. So Link being with Medli, while from a distance could be kinda cute, I just don't really care for up close.
Komali's feelings toward Medli--if they can even be regarded as romantic which I'm not sure they can--are unrequited, and if Medli has feelings toward him in any way, are pushed aside because her duty as a sage (and before that, Valoo's attendant) is of the utmost importance. That was the point of whole scene with Komali being left behind with his flower.
Medli is a cool character though, but I don't think she needs to be shipped with anyone. May overshadow her sense of duty--a core aspect of her character--if she commits to a person.