I assumed that she was going to say something like, "I'm afraid I must destroy the mirror now, but I'll miss you." but couldn't bring herself to say it because it was painful... so she just said what she usually does before going, "See you later." I'm not so sure she really did miss Link... maybe she just wanted it seem so. She might have just broken the mirror to make sure she'd have rule of that land all to herself.
Even if she did love Link, I don't think they would have let her say that specific phrase. Nintendo goes out of their way to keep Link's affections vague so fans can decide for themselves which girl they'd like to see him with.
I suppose my main problem with the idea that Midna could have loved Link is... I don't think Midna is capable of caring about anyone. She strikes me as heartless, and I never quite trusted her. I never got over the feeling that she was manipulating Link for her own ends. She may have admitted to it and apologized, but that was probably to keep Link from turning on her when he figured it out (which he was close to doing). I expected her to betray me to Zant at the end, and then I expected her to betray me again to Ganondorf... I was surprised when she didn't. That was probably just because she didn't want to share any power, though.
The thing is, Midna is a Twili, and the Twili are... well, descendants of the most evil, self-centered magic users ever. It's hard to believe the apple would fall far from the tree. Also, when you start the game, you get a distinct Machiavellian sense from her. I know she can think that way, and I do appreciate her intelligence. She thinks kind of like me, actually, and I would never trust anyone who thinks like me. Especially not one that thinks like me, and isn't as sensitive... yikes. Midna isn't exactly sensitive or expressive, you know. She's rather cold.
I personally would have found the game more fun if Midna had betrayed me to Zant at Lakebed Temple or in the Palace of Twilight (or even Ganondorf at the end). The plot twist and the feeling of betrayal you'd get after having travelled with her that long would be... amazing. It would have been quite refreshing, actually. Just having her seem mentally and emotionally capable of betrayal but yet remaining loyal to the end seems so... dull and silly. If she was going to remain loyal to the end, why not have her be helpful and polite like Navi? Why bother creating a character that almost feels like a rival to the player in terms of controlling Link and observing the nature of puzzles... if they never betray you?
I don't know, maybe there was something about her that I just didn't "get." A lot of people like her and think she loved Link, and I don't understand why.