That's exactly how I felt about them too, which is why I decided to pair them up. I think they really balance each other out, and would make a great couple. After all, opposites attract.
Both of them have had such tragic lives, lost the ones they loved, and blamed themselves for it. But they acted out on their tragedies in radically different ways. Thane vowed to live his life doing good, and redeeming his sins. Whereas Jack just stopped caring about anyone or anything. And made her self cold to the world.
So since their situations are basically the same, but their views are radically different, and to extremes. I figured they might make the perfect match. And yeah, they are the two characters i felt for most in the game.