That kind of critical feedback is exactly what I need to hear, as it's really hard to stay objective after staring at my own work for hours upon hours. I'll address them one by one.
1: That cobblestone texture simply does not align well, unless I changed the width of the streets, which I am loathe to do at this point. I may conceivably change it, though most other cobblestone textures I have seen are just as non-directional.
2: I agree, the roof's interior should be flat wood planks or somesuch. I've changed this in some places, but not in the area I took that shot in.
3: Roofs at 45 degrees, I assume you are referring to
http://img208.imageshack.us/img208/8640/dp000006nb2.jpg ? This can be rectified with clever stretching, though I don't think you'd notice it in game as much, as you would be seeing the roofs from street level most of the time.
Regarding the windows... I can assure you that you can, in fact, go inside all of the buildings. They are lit with a point light of delay 2 (1/x^2 falloff), light 32 or 23 (depending on size of the window) right in front of the window. In other Nehahra engines, this looked fine, but the overbright gamma of darkplaces oversaturates the window and makes it look too bright, even though the light is not traveling too far. For certain windows where the light ought to travel farther and spill out into the street, I intend to try delay 1, 1/x falloff, though I haven't done so yet.
The window frames, and the wood "X" frames, used to be made from individual brushes. The X frame prefabs were 11 brushes each. Realizing this was insanity, I made up flat textures in photoshop and reduced my brushcount by at least 1000. Do you mean the windows should be inset on the inside or outside? Given the open nature of this map, I'm trying to keep surfaces flat where possible. In certain places where gameplay dictates, I do intend to make the windows transparent and breakable, but it's not realistic to have every one be like that.
I like the idea of chimneys for atmosphere and realism, I'll look into where some more would look good. Do you see the one here?
http://img529.imageshack.us/img529/6975/dp000002li4.jpg The misc_smokemaker trails are still moving a bit fast to be realistic, but they are there.
I'm aware it's not your typical quake scene, I've never been big into blood and spikes style maps myself, I think it will become appropriate in context.