Wow, thank you so much for such a detailed and thought-out answer, it really means a lot!
I haven't had any prior experience in hammer or pretty much any 3d mapmaking, the only experience I had was the few basic test maps I made prior to this to learn the ropes. I think that inexperience is a big part of a number of some of those issues you mentioned, but I definitely learned a ton by doing this and have a number of things I think I can improve upon in the future.
I did use areaportals wherever I thought was appropriate, namely in each of the entrances to the building and in various doorways and windows and such. I didn't use any areaportalwindows, however, even though you're definitely right in that there's probably a couple places where they'd be applicable.
Your comment about the flickering lights is something that never even occurred to me, and even though they don't bother me as much it would probably be worthwhile to slow them down and to make them less bright as well.
I like the idea about the fences being pulled down, and I definitely agree that right now it's a little unrealistic to have the zombies just spawn around them. It's just always a little bit of a design tradeoff I think, since that also introduces invisible walls... I can probably get away with making some of the fences be pushed down towards the interior of the map, so that a player couldn't jump out but one could imagine a zombie climbing up it like a ramp.
You're also definitely right about the key objectives; once I learned how to randomly spawn keys and a welding torch I admittedly copied and pasted that for the other secret areas lol. I like the exploding gascan idea and it might be worthwhile to make one secret be accessible only by welding torch rather than key/welding torch.
I clipped as much as I could, and really the only thing I can think of that can be significantly exploited is the table in A. My issue with clipping certain things though is that from a player's perspective it's extremely frustrating to be trapped against a wall or a corner by zombies because you can't jump over an object that in real life you very easily could vault over. I'll look into it a little more though and see if I can find some reasonable stuff to clip.
As part of my own thoughts, I think one of the biggest issues with the gameplay of it right now are that most of the objective entrances are pretty close together---especially B---which makes it easy to defend the point just by corralling the zombies outside the objective and just meleeing them. I think it'd be a ton of work to redesign and restructure those parts of the map though, so I think it'll probably just be something I keep in mind for the future...
Thank you again for your input and I'm glad you found it interesting!