ok, i had a look around it, and have some comments for you:
+ Layout: many big rooms, with lots of repeating sections is a bit bland, more detail is needed i think, not just for prettiness but for places to hide the alien base, Also put in some landmarks to help people find their way around. Some vents maybe.
+ Lighting:/Texturing needs more lights, more color, more detail. I think you should stick to a consistent color scheme instead of having rather luminuous doors of primary colors. Textures are a bit bland, but you know that ;]. You could also make your own skybox (with terragen) than use that one.
+ perf: will be poor in those big rooms with bases/players in there.
Otherwise, its not all that bad, nice use of patches.