That commanders idea is really cool and i think they can be unlocked by levels.
My ideas:
New slots:
Armor slot
Each ship can buy many kinds of armor like uranium, titanium, vanadium armor etc. Each armor type will differently decrease ship's speed.
Shield slot
Ships can have more types of shields such as small, medium, big, ultra, small projectile shield (less damage from projectile weapons) etc.
Thruster slot
These thrusters can make ship be more agile. Thruster types: ion, fusion, thermal, plaema, photon, yamato, goliath, behemoth thruster etc.
Better level system:
This system will be much better because in normal you can onlh level up by battle score and this system:
Each completed mission and destroyed ship/fighter/factory will give you xp.
Level bar can be seen in battle at the top side of the screen.
Weapons, ships, armors, shields, thrusters and fighter will be unlockable by levels.
