I would love to see equipment for crew members. For example:
Vacuum suit: immune to oxygen loss
Fire suit: prevents health loss from fires
Extinguisher: speeds up fire suppression
Repair kit: speeds up repair
Medical Kit: heal other crew members in the same room.
Personal Teleporter: teleports crew member to medical bay on critical health (even from enemy ship: single use)
Weapons and armour for hand to hand or ranged combat...
Bombs: to plant in boarding missions to take out enemy systems...
I would like to see longer skill paths or even skill trees for crew members. Perhaps racial specialisation in different areas (Mantids: weapon control and combat, Rock Dudes: shields etc)
I would like to see skill progression (and stations) in the drone area (faster drones?), medical bay and other areas.
PLEASE can you let us choose which crew member to commit to mission so my top skilled pilot is not randomly killed by space spiders or disease! This could be paired with the equipment ideas above to great effect I think

Also I ran into a problem with a game where I was using the number keys to select weapons and accidentally selected an option in a dialogue box that popped-up (I accepted the surrender of a ship that I wanted to destroy). Seems it might be worth deactivating the use of number keys with dialogue boxes, or introducing a re-mapping.