There are basically five areas to fight in; you need a sixth badly (and maybe even a seventh). Also, spreading out the map a bit should help.
Take out this lame vent (Pic 1) and replace it with a door here (Pic 2) that leads back to another door here (Pic 3) through a couple hallways and maybe a little room.
Extend these two hallways, forcing the front and back areas further apart. Just recess the elevator in the back room instead of having it pop out; that can give you 128 units easily. You can also stretch these hallways a bit by making them open a little further along the front area.
A lot of your doorways are vertically-challenged, and they don't need to be as tight either. Try making your narrow doorways 64 instead of 48, and your wider ones 96 instead of 64.
Try replacing this junk with a row of pillars instead. More usable as cover, and should look nicer.
Missing texture here, looks like a gap in the brushwork there. Minor details and more relevant to something closer to release but why not.
Your pillars are fat and ugly. I realize this is pretty much the way it was in Perfect Dark. I'll refer you to Vitruvius' Ten Books on Architecture, specifically the part about temples. Broadly, make pillars six or seven times as tall as the width of their footprints, and make the gaps between them two to two and a half times their width. Two-thousand-year-old Hellenistic cruft? Maybe.
It looks like the height of your first floor walls is pretty uniformly just over 128. Working on the gridlines will make keeping your brushwork solid much easier. Making your walls 128 high instead of what looks like about 132 will make your texturing much easier.
Put doorframes on the transitions between areas, especially between hallways and the main rooms. They don't have to be big (4 units might be plenty, maybe a bit more down from the ceiling). With your doorframes in place, don't be afraid to vary the height of the ceiling from one area to another.
Smooth out this stairway a lot. The slope looks good at about 1:2 (but could probably safely go to 2:3 if needed). The steps are way too high though. 10 units would be the max IMO. A good reference from reality is that houses usually have 12-14 steps from one floor to another, other buildings could be 16-20 easily.
The elevator can get hung up because the doors and concrete are not flush. Try making them even if possible. Better would be to have a pair of doors parented to the elevator on the inside, and independent doors on the outside (just set both pair off with the same trigger).
It's tough to say to start something from scratch, but the whole map will need to be retextured at some point anyway. Pick (or create) a smooth, desaturated texture and texture the whole map with it so you can see what you really have with your brushwork and lighting.
As far as the lighting goes, take out (or disable) the lights that you have, and see what you can do with light_environment. Unless you're going to change to a daytime sky (or one with a moon), just disable the direct light and use the ambient. Get it to where you want it, then compile once with -final to see what it's going to look like. If the glass skylights in the back/main room let the light through, I think you could get about 2/3 of the map lit with ambient from the skybox. That's not to say don't use other lights in these areas, but just see what you can do with it; VRAD never fails to impress.
One problem with the lighting you have already is that it's very saturated in some areas. Try staying closer to white even when you want colored light.
The point/prop lights can be done a lot better. You did pretty well with the two posts out by the body armour. The rest not so much. First thing, forget about lightglows and spotlights until much later. Identify where you need some light, place your prop/texture, then cast light from it. Repeat. Just try to figure out what will fit best (aesthetically) in each area, and use as much of it as you need. Use a light entity for things like cagelights and bare bulbs. Use a light_spot for lights that are in some kind of fixture. Don't stick with the default values for light_spot, for something like fluorescent lights you want to make the inner/bright angle fairly large (60+) and the outer angle closer to 90. If you make these the right brightness, VRAD should bounce enough light back up off the floor to light the ceilings fine. Same goes for floodlights, although you'll probably want a tighter angle.
Personally I think that round light fixture you've used in a few places doesn't go well at all. Floodlights would definitely do well in the front/outdoor area. In areas where you have ceiling tiles, fluorescent light textures (like one that's in goldeneye already) are probably better than a prop. lights.rad controls how much light each texture casts.
This level calls for custom textures big-time. Some areas are OK, others are hideous. I'm thinking smooth concrete in the front, polished stone in the back, and clean, sharp textures like in de_nightfever in between. But that's just me.
I realize the tone of this post may seem a bit down; it isn't meant to be. This is way better than what I started out doing with Hammer.
Feel free to send me a later version if you want someone to look it over before release.
