Jimmy nuetron is more likable. If we're just talking about the main characters, Jimmy is far more developed and entertaining.
Actually, I don't even know if this is a fair comparison because Jimmy was made to be a character. Dexter is just, a concept, an idea. Dexter fits the “genius boy” cliche so tightly that he even has a German accent. I like Dexter's lab, but dexter isn't a character the way Jimmy is