Thinking about Jonathan some more; while I do think he isn't very interesting or particularly filled with depth compared to the other Jojos, the big thing he has going for him is that he's a dude you just can't really hate. He exudes this good vibe that makes you like him despite not being a very unique protagonist, especially when he's surrounded by nasty characters like Dio and the rest of Phantom Blood's tone is somewhat bleak as he's put into tragedy after tragedy. That's probably what makes people so quick to defend him from people calling him a bad protagonist for not being interesting enough- he's just... a likable guy.