I didn't read the rest of the thread, so some of my ideas may have been debated to death, but I lay them here for your perusal:
Saru - After his work bridging the gap with Ni'Var and being involved with other worlds after the collapse of the Emerald Chain, the latter obviously written in, the Federation decides to make Saru a special envoy to reach out to the planets Discovery visits. This wouldn't be a step down for him and allows him to still be on the same level of Burnham and have those discussions. It also is a natural step for him. He wanted to learn to be a Captain from Georgiou, but he realizes she was also a diplomat and this could be another way to honour her.
Stamets - He can logically understand why Burnham blew him out a window, but he can't emotionally forgive her. His comments to her about leaving all they knew to follow her here and she almost let his husband die. He was plucked out of wherever to develop the spore drive and since then, he's had a lot of pain. This will be a source of on-going tension that can come eventually to a head.
Definite Roles - Pick a first officer and don't make it Tilly.
Secondary Characters - I was beating this drum all season. I understand Burnham is the star, but the writers also moved toward a "family" feeling amongst the crew and we know barely anything about anyone outside of Burnham, Saru & Tilly, and to a lesser extent, Stamets & Culber. Burnham can still drive the action, but bring the secondary characters in and build them through a natural part of the story. We literally have no idea why they all chose to follow Burnham. Right now, it is left as if she is anointed or something.
Storyline - Another drum I beat all season was that the Burn didn't need to be solved this season as long as it was moved forward. I also didn't buy that the Emerald Chain would simply collapse because Osyraa was killed. The season does not need to have every single storyline buttoned up at the end of the season. It also seemed like a lot of former member worlds were ready to sign back up again fairly easily. The antagonist of my season four would be a collection of former members that decide the Federation is "morally bankrupt" for the way it handled its response to the Burn and decide to align.