just some random thoughts on the character class system.
If all the player's characters spawned in with a basic inventory (pistol, small welder no armour) so you would always have the ability to fight and repair then had to gather resource to upgrade your players by buying better equipment from lockers or something. Maybe 3? levels/tiers of each (weapon,armour,repair,other?) but you could only carry 1 Lvl 3 1 Lvl 2 1 Lvl 1 this would would give you the ability to specialise without ever loosing the ability to function as a team member.
this has some flaws i know (why do you pay for things already on your ship )
XP points !!! instead of resource gained by mining building and teamwork (building on mothership gives bonus or something) might encourage teamwork.
im done..........for now