I would definitely say I prefer Medli, just because her use in the Earth Temple was far greater than Makar's use in the Wind Temple.
I love how the Earth Temple basically expanded on Ocarina of Time's Spirit Temple in terms of the use of the Mirror Shield. When I first played through Wind Waker, I had already beaten Ocarina, so when Medli's Mirror Shield was first used in the Earth Temple, I had a fairly good guess what the dungeon item would be, and I was excited to see how it would be used. I was not disappointed. The mirror puzzles in the Earth Temple are pure genius, making use of Medli in order to make more complex puzzles, where multiple mirrors had to be positioned. In particular, the Mirror Room of the Earth Temple was quite intriguing and fun.
Makar was not used well enough for me to like him. His controls were awkward, and he ended up being a nuisance most of the time, constantly getting trapped and needing to be saved. He came in handy one or two times, but most of the time it was just annoying to have to keep track of him.
Plus, Medli had a better developed character. When she is first introduced, she seems like a lowly attendant, but it is very interesting to see her relationship with Komali evolve and unfold, cumulating when she decides to leave with Link to become the Ssge of Earth, leaving Komali behind.
Medli was far more creative in use and as a character, so I would definitely say that I prefer her.