MOVED FROM COMMENTS:
Well, on the top floor, that big pnematic door could open up into more rooms. There's a lot of space, but considering the exterior of the ship is not too far away from it, perhaps make a Captain's Quarters? Don't think anyone'd be angry if you used some Mass Effect stuff for props.

On that same floor, where it has "Deck 01" opposite the elevator, could probably copypaste that big room down that hall next to it in there and give it a door that won't obstruct the deck number.

One floor down, the Medbay has plenty of empty space between it, the outside, and the hangar that it could be much much larger. Obviously without touching the other rooms.

Officer's head is fine, if a little unnecessary, but it makes sense for an actual naval ship.

Officer quarters are both fairly cramped. If you add that Captain's quarters, though, you could turn the CO room into another Officer's quarters. Two "officers" per quarters makes sense for me, and much as with all the other rooms, there's a lot of empty space between them and the exterior that could make the rooms much less cramped. The current CO quarters even has some empty space between it and the batteries that could be utilized, and it'd probably be good to take the corner next to the door out too.

Storage room is fine.

The enlisted barracks are the biggest issue I've seen. Despite sounding like a broken record, there's a lot of space that could be utilized. Move it as far as it can to to the exterior, and take the bunks and line them against the right and left wall after, evenly spaced between. It'd look much less cramped, and a million times nicer. If there's too many bunks, it'd be alright to get rid of them. Most people, at least in the RP community, don't really take the number of beds into account. That glass floor is a bit superfluous too. Perhaps add a ladder in the corner and a small cubby down there with a grate separating instead of glass?

Lounge can be much, much bigger, especially taller, and the yellow lights should be toned down.Floor in there is a bit odd, too. Not sure what that center bit is. Mass Effect props could be used in the expanded room here, as well, making it more of a Rec Room, or just make it bigger and leave that to the user.

Third floor is the very definition of empty space. The cool red heat linings in the engine room are awesome, but if you kept those and made other rooms behind them, perhaps some secret stowaway rooms or maybe move the battery down there, giving more space to make the battery look powerful?

Otherwise, it's all good. Hangar's great, bridge's great, and overall the ship looks nice. I just feel like it could be much less cramped in all those ways, and that more rooms are always awesome. Gives room for people to build armories, shooting ranges, and more.

Also, looking at it, there is no engine room. The heat things downstairs are for the main gun, my b. Could make the captain quarters upstairs, and perhaps a ladder next to it that would lead down into an actual engine room.

Sorry, one last one, the second floor again. Those terminals near the end could be pushed further down and you could make another large quarters room. Perhaps one for soldiers and another for naval crew?

Sorry for filling the comments.