With Canon potentially a problem for later shows, if we revisit the Klingons or the Federation, I would like season 3 to be a bottle season about the consequences of jumping to the future.
Burnham has lost Sarek, her sounding board in times of loss and needing introspection. She lost Tyler, who has healed here and helped her come center. She should face danger and rely on her own merits, a struggle that lasts the season. There should be some mourning. Homesick should be overt in Tilly, like last season's psychotic theme. She has just lost a promising career, the potential Captain. Saru did this when he left his people, he should be a guide, for the crew. The entire crew is down the rabbit hole, again.
There are logistical concerns like sources of power and food, deciding whether to stay on Discovery, or find a new home. While doing this, they should face an arc through the season, a bad, that reflects these emotions of sadness and loss, and in all their missions, big and small.
So, how does one cope with loss?
--shutting down emotionally.
--escape through drugs and temporary fixes, become out of balance. I think the most potential for a theme lies here.
--by neglecting the present for the past.
--by seeking emotional comfort by using someone, a love interest that is shallow.
They chose this, but the decision should resonate throughout the season.