I'd probably go with wood for the skeleton, foam board for the main floors and plastic for the vertical structures/hull/doors/tables/consoles/etc. Of course use screws and epoxy to hold it all together along with a dremel and hacksaw to cut the plastic.

If you check out my warehouse in the pictures archive, you'll see that it's very heavy just from looking at it because it's all wood. That building is relatively small compared to what you're planning and I'm not a big fan of moving it as it is.