Dear Sad and Confused-
Your question actually makes me sad for you, because situations like this always happen and there is nothing you can do but move on.
As women, we often speak in our own language, so if I may, I will do my best at a translation, she is really saying "I know you are the best possible guy for me in my rational mind, but I don't want love to be rational."
You probably do get along well, and someday she might think back and wonder how she let such a good guy go, but nothing can make her realize it except using her own judgment, making mistakes, and learning from those mistakes.
Watch Her Fall in Love
In the meantime you get to be her "friend" and watch her fall in love with somebody else. It's not fair, it's not right, but sometimes that's just the way it goes.
I had to wait what felt like forever before my boyfriend showed any interest in me. At times, I was a complete basket case because it's so frustrating when somebody keeps you at arms' length, but you either wait around for what could be forever, or you move on.
I waited a few months I don't know that I would've waited much longer.