Ok, here is the list that you wanted of things that can be inproved on:
Bridge:
-Have the weps consle be able to arm/dissarm the rear torpeto tubes
-Have self distruct butten built into the captions chair
-Let the hyperdrive overheat/explode if left on to long, like 5 min.
-Charging consle for the main weps array?
Weps:
-Main torpeto tubes need to fire somthing
-Torpeto tubes need to be able to be charged
-Main torpeto array?
Second floor/bunks:
-lights on/off?
-some kind of privacey?
-some kind of bulkhead
-close the floor up (you can see through parts of it next to the bunks)
General:
-where is the power generator?
-where does the life support come from?
-if there is a breach in the hallway going to the airlock, how will the bridge not be depresherised?
I will inprove on this. This is just to give you a general idea. Sorry about my spelling.