I prefer Midna solely because I feel she formed a closer bond with Link than what he had with Ilia, but she's definitely a close second for me and I only recently decided that Midna would be a good fit for Link in the first place . But I'm glad to meet someone else who appreciates Ilia, she gets so much more hate than she deserves!
It's a great manga, I'd totally recommend it if you'd like to read a more in-depth version of the story.