(General, not shipping) The Doctor didn't mean to get involved with the Winchesters. They're into all the wrong things: the killing kind of things. But now he's attached, but that means he's got to deal with the consequences. Because getting involved with the Winchesters means he may lose one of them.

Instead of Dean being the jock and Cas the nerd, it's the other way around. Dean has a crush on Cas who is a popular kid in their High School. Dean has to take care of little Sammy and he is constantly mocked at school just for being a nerd. [Destiel and Sabriel]

Before Jor-El can allow Clark to defeat Darkseid, he must face another trail. Clark must learn to fight evil Supernatural forces. In order to do that, he switches the bodies of Clark Kent and Dean Winchester. Clark learns what it means to be a Hunter, while Dean learns what it means to be a superhero.

(Not shipping) Dean has never met anyone like the Doctor before. For that matter, the Doctor hasn't met anyone like Dean. They keep meeting out of order, too, and that only complicates what is already a rocky relationship. The Doctor isn't human, after all, and he has a tendency to show up when trouble is brewing.