I think the interesting thing about Jack is that her defining character trait is hatred. Not of other people, but of herself. Every action she takes is coldly calculated to make other people hate her and, in this way, help feed into her own low self-image.
When you think back to all the initial reactions when she was first revealed: "Ugh, she's ugly. Why doesn't she grow some hair? And what's with those ugly tattoos? Why doesn't she put on a shirt?" In a way, I'm sure that's exactly what she's going for. While she would probably claim that it's just her style, everything about her is calculated to be as initially off-putting as possible.
But suppose you get past that, or maybe find that kind of unconventional look attractive? Well, that's where her attitude comes in. As abrasive and vulgar as possible, because she doesn't see herself as any better than that. Nobody could possibly care about somebody as horrible as her, and even if they managed to fool themselves for a while into thinking they could, she'll set them straight.
The significance of Jack's loyalty mission didn't really strike me right away, but upon further reflection, it really says everything there is to say about her character in a short span of time. Pretty much all the evidence you find shows that Jack was kept separate and treated differently than the other children because she was special. She was stronger than the rest of them, and the most important subject there.
But Jack can't accept this. Obviously she was treated the worst, because everyone there hated her. They enjoyed tormenting her and treating her like garbage, because that's really all she deserves. When she broke out, obviously everyone attacked her because they just couldn't wait to show how much they hated her. The idea that that hatred might have been because she was the important one, and was regarded as something special, just doesn't compute with the image of herself she's built up over the years.
And that's why she does her best to turn away Shepard. She needs to believe that she's as worthless and horrible as her own self-image. The idea that someone could look past all the walls she's built up and see that's there's something of worth underneath it all makes her confront her own image of herself. And the scariest thought of all: not only that somebody could actually care about the piece of trash she thinks she is, but would be willing to DIE to keep her alive, throws her entire world-view out of whack.
This is why, in a lot of ways, I think the Jack romance is one of the best. It's easy to go after the slightly-nerdy, shy girl with a long-hidden crush. Or the well-built, genetically perfect exotic vixen. But to keep persisting against somebody who is trying with all her might to make you hate her, and force her to see that she could be cared about... even loved, that's a little harder.
And if there's anything a guy like Shepard likes, it's a challenge.