I agree it's not what I would have expected but there may be a method to the madness.
It's possible someone thought by making AJ a team captain they'd draw him out of his shell and get him to be more vocal and more invested in the team as a whole. There's not much need to do that with Kyle. He bleeds navy and orange already and he also doesn't need a "C" on his jersey to be vocal and seen as a team leader.
I'm a bit more surprised by McPhee seeing as how he'll miss at least 6 games but maybe someone will pinch hit for him until he returns to the active roster. McManis makes sense as a STeam captain as well.
It could also be that Long has taken on the role of Team Enforcer.
A bit more seriously, sometimes the most passionate people are not the best leaders because of that passion. This could be part of the reason as well.
He and our new OL Josh "Salty" Sitton. We now have an OG pairing of "Salty" Sitton and "Kong" Long surrounding Cody "Wonder if he can play OC too" Whitehair.