Link and Midna, definitely. Aside from her just being my favorite video game character of all time, I have to say that I really felt a connection between those two. As you mentioned in the article, there are hints all over the place suggesting this.

Now, I s'pose I could see Link and Ilia getting together, but Midna just seems like a much better fit for Link. While her personality itself is a key factor in that, the growth of their relationship just seemed more natural, to me. It's something that, despite how the game ended, I would love to be explored in a future Zelda game (without focusing too much on it, of course).