Basically it would be cool if the whole team/squad/organisation could travel around with one big mothership, containing multiple smaller ships and hovercrafts etc.
Pros:
Possible social interactions while flying
Easier to defend (against possible threats)
More epic gameplay if you encounter a (possible) threat
What would be needed:
Hangar doors / airlocks
Docking stations
Recharge stations (If this fits in the energy system)
Epic sirenes and alert systems (e.g. red/yellow alert) to alert the team/squad/organisation to go on combat-station -> this will create a more epic atmosphere