Thank you, We really appreciate your opinion. This is our first game and our first game jam, so receiving feedback like this means a lot to us.
The upgrade system definitely wasn't explained very well, although the weapon upgrade is pretty self-explanatory.
The idea is that every time you return to the ship, you consume resources. The mechanic reduces the number of parts consumed each time you return, the cook reduces the amount of food consumed, and the medic increases the health of every NPC on the ship, since they have health and can eventually die from starvation.