Downloaded and stopped playing it when the game crashed searching for "custom.wad" on the map pls11.bsp, from what I played, I can say is that your mod needs serious work, I was going fine until the female assassin's ambush on the container area, with those gasworks-like towers, I had to cheat that part and a lot of some other parts of the mod, also, I was playing on Easy. Judging for the screenshots that you put on Moddb, the Mod looks awesome, that's why I downloaded it, but playing it, it's like playing another mod, A very, very blocky mod with tons of enemy npc's waiting for you at every corner of the maps, it got so boring that I stopped playing after the crash. As for your mapping skills, the part I played is very bad, the maps are very blocky, so much blocky, the only nice part I can spot for now is that HL-Uplink-Like rocky hallways, which still too narrow and very dificult to navigate trough. The boring feel was lost on the Road Trip chapter, It was nice to drive a func_train car, even if you can't control the car, the gameplay changed from the same '(A)Kill-a-couple-of-monsters-in-the-next-corner, (B)Recharge-your-health-and-suit, (C)Back to (A)', but again, I think the whole US Army was in that map.
Also another thing, your mod archive have a LOT of unecessary files, you copied TWO times the whole HL sound files, one time in your Pulse folder, another time in the pak file, you should get rid of that stuff, your mod will go like from 150 mb to 30, 20 mb, making much more easier to download it, especially on Moddb's slow mirror.
Ok, I managed to play the rest of the maps on the Mod while I was posting this, after faking many not included .wad files, I saw that you improved a lot your mapping after pls11, the maps are now less blocky, altough still full of npc's every corner, its a improvement, now that you're mapping better, you should improve your entity setup and gameplay of the maps, also, another thing I forgot to mention, I didn't saw the r_speeds counting on your maps, but most of them was like 30, 20 fps on my computer, and it's not a crappy computer (c2 duo with Hd 4850), I nocliped and saw what I expecting, the no-use of the Null texture, and the indoor maps doesn't need so much the null texture, but still lagging, so I assume you didn't compiled your maps with full vis or even normal vis, you should do that on the final version.
Well, It's clearly a beta or alpha, it's a very unfinished work, needs serious work before releasing the final, but for being a one-man mod, I respect your work and I know that you worked hard on this one, don't feel sad because of some bugs and issues, remember, these are just critcism that you can use freely to improve much more your mod and making a masterpiece, keep working hard on it and good luck!.
Edit: The website is f***ing nice, very professional, I can't say a thing about it, also your plot is epic.
