Haytham and Connor never really got a chance to get to know one another. While I'm sure chasing and killing people together will tell you a lot about a person, it's important to experience calmer more controlled settings.

John knows he has an unusual relationship with his flatmate. He knows their friendship is complicated. And yes, he knows everyone assumes he's in a relationship with Sherlock Holmes. But he's not. Obviously. It's not like that. John would know. Right?