Good improvements, some nice stuff in here. The starting area makes a lot more sense now.
A few things I noticed:
When you start, GZdoom says this at the console:
Unknown flat NFTL65GR
You can get the armour in the armoury by bumping against the wall - no need to open the little door.
The invisible teleport that fakes room over room is far from invisible because the area you teleport to looks different enough compared to the area you teleport from for there to be a visible jump in texture and sector appearance.
The teleport that you activate is a bit odd in the way if functions. Usually, you have run right off the other side of it before freezes you and it just feels a bit strange and clunky. Also, I know it is far from a completed map, but it would be nice to be able to get back from the destination.
You've used portals to simulate glass-covered pits in a few places. When looked at from some angles these can show glitches. Seeing as how this is for GZdoom, why no do away with them totally and use genuine 3D pits?
I just took this screen shot because I thought the area looked cool.
Although, I think I'd have made the UAC logo on the floor shiny too.
There are some areas where texture alignment, or putting borders between textures would improve things. These are similar but different textures that don't look good butted right against each other.
And some are just badly aligned
