This map is considerably better than your previous one.
I'm not a mapper or game designer, so I'm unsure if I'm qualified to offer advice, but here we go...
I see you have implemented a difficulty selection menu. That's pretty nice. However, one thing I believe you could improve in this regard, is "adapting" the level to the difficulty. In the official quake maps (and in many well made fan maps), the amount of enemies, quantity and/or placement of pick ups, weapons, etc. change on difficulty. So if you play a map on normal, and then play it another time on hard, you will see that the enemies are placed differently or that there are stronger enemies or even a higher amount of them.
I think you could look into that.
The picture below is a screenshot of a door. I believe this door could've been better, as when playing the map I didn't know it was a door at all. In an attempt to tell the player that it was a door, you cut holes on the walls, but I believe that's not enough. Maybe a different texture could have helped?
picture representing the unclear door
One bug I found, is that in order to select the nightmare difficulty, one has to jump on the portal. Simply walking towards it doesn't work. I'm not sure how quake mapping works (as I said I'm not a mapper), but I think there's some area that if the player passes through it, a skill change takes place. Perhaps this "area" the player must pass through should be placed lower?
portal to nightmare difficulty
One last complaint, is that the messages that appear on the center of the screen seem to be triggered too many times. The messages in question are "intruder alert" and "open the plane". Maybe there's a bug that they are getting over-triggered?
But yeah, that's about it.
btw, I found your weapon cutouts in the armory really cute. Did you make them yourself?