Aight, played it and recorded a demo. Comments and thoughts during the playthrough, overall it was good, but needs some work. Most importantly, the layout is pretty confusing, probably substantiated by the same-ish look of most of the areas. This could probably be avoided by varying the textures a little, as I also note during the demo, and making the rooms more unique in other ways. I also noticed a lot of misaligned textures and corners of brushes extruding through walls and such, especially with the curved pipes (which were nice by the way!), probably caused by the vertices not being exactly on grid - but I know how difficult such structures are to work with and such problems are almost impossible to avoid. I didn't really get stuck on any architecture either, so I guess it isn't more than just an aesthetic problem.
Also, I think you should indeed tone down the colored lights a little, as in some areas they were overdone - make them more subtle, and also add some more neat, subtle light/shadow effects like I noted near the exit in the demo - it works wonders for atmosphere! And yes, I thought it was a bit too dark overall as well.
On the gameplay side of things, I thought it was pretty good, except for the confusing layout that makes it easy to get lost. I found it a bit empty though, maybe add some more enemies and interesting ambushes, perhaps some powerups to keep the action flowing?
Pretty good stuff, looking forward to more. Oh and yes, the demo of course:
http://www.quaketastic.com/upload/files/demos/grad098_bern.7z