I think at first we will only be facing Cohort and the fact that Alec is trying to resolve the Shadowhunters' split. Until «The Black Volume of the Dead», we're unlikely to touch much on Magnus or the threats from his father. But the closer we get to “The Eldest Curses”, the darker the story will get for Magnus. I think he'll be in danger again because his father will try to devour him (maybe?). Things will get a million times worse because Alec will again want to save him at all costs, but now Magnus has a strong argument - «You're the Consul now, everyone is counting on you»...
As for the good - I expect a lot of progress in Malec's relationship with the kids. Now that they're older and they even have Tavvy, family interaction could get a lot more interesting and funny.