I dunno who will be, but I think in terms of how the show works, Burnham basically has to be the captain now.
Basically the problem is this: SMG is the lead, but Burnham hasn't been the captain. Thus they need to find ways to make her have the most lines in every episode, despite the fact that she isn't technically the final authority figure. The way the series has done this to a large degree is by giving her an extensive backstory and having lots of random stuff happen to her. In the last season there were episodes where her backstory with Spock - even if well scripted and acted - was basically padding to ensure that she maintained a higher line count than Pike or someone else. And even given this, there were still a handful of weird situations where Pike despite outranking her just deferred to her authority when she said something.
The problem they have for season 3 is the backstory is gone - or more or less irrelevant. I guess they can string out a quest to reunite with her mama, but all the stuff with Spock, Sarek, Amanda, etc will presumably not matter any longer. The easiest way to ensure she has the lead in lines per episode is to make the buck stop with her character, and the easiest way to do that is by making her sit in the chair.