It really is hard I agree, with such a broad spread of rank it's hard to put everyone in the same scene. I'm happy for either idea, but I find it hard to see a way for the entire group to be in a scene at once without something major happening to level out the power structure of the ship.
One reboot idea would be for Jack to not be ship commander, have that role filled by an NPC. Then making sure everyone else has a similar level of command, or at least some kind of "expert adviser" role. We get given briefings as a group then there is a reason to work together as a team to get those things done.
If this is intended to continue as a "PC's with a Cap ship" idea then the other option is promote everyone to a high position of command within the crew. It's still going to have the problem of some PC's not working with others regularly.
I guess the question that needs answering is "how do you get indivuals from all over a ship to be working together regularly?"
Away Missions.
Ship crash with very few survivors.
Put everyone in the same unit, or the same division (all Marines, all within Engineering, all within Fighters group)
Put everyone on the same command level.
Unite the group with a common an probably secret goal that's more important than command (a secret spy mission, building a rebellion within th crew, anti espionage, etc)
I don't really mind which way it goes, but I don't want to play a Solo campaign with occasional cameos...