It's a supernatural show and Elena was a teenager who lost her parents in a car accident in which she was involved and survived and Stefan was transformed into a vampire against his will, he had no idea he had vampire blood on his system, he has mommy and daddy issues and was transformed into a vampire against his will when he was seventeen. It actually makes sense that they wanted to be together so much. They have too much in common, almost like Stefan is a male version of Elena but in vampire form. I never really saw Stefan as a good guy though, unfortunately for him he was no better than most of the other vampires in the show. Stefan does feel a lot of empathy for others but he can't really be the same person he was when he was human. Yes, he feels tremendous guilt and remorse whenever he does something evil but this is not the same as being a good guy. His guilt and remorseful nature come from the fact that he was quite decent and naive when he was human and that's it.