So, I've been trying this out for a bit. Admittedly, I made myself a map with my favourite map editor that allowed me to check out what all the assemblies look like and I have to say it has renewed my appreciation all over again for how much work has gone into this because holy crap! :o There are so many new sprites, not just for the new weapons, but for all the variations in assemblies for the new weapons too! (Yeah, I know I'm late to the party here, but I still think it's really cool) :) I especially like the Gothic set bonus; that was a nice touch. ;) I think my favourite character is the technician... even though everyone else has more obvious combat benefits, the technician gives you more access to the more interesting weapons. :)
With so many options, I imagine it's next to impossible to keep it all balanced, but the weapons that stand out the most in my memory as over-powered would be the railgun, (I think it could stand to fire a little slower) and the automatic shotgun. (I got the double variant and it shredded a Cyberdemon in very short order, though, it did take nearly a hundred shells) Speaking of Cyberdemons, I think they do way too much damage now; one brought me from 200% health to zero in one hit, even with armour. (Not fireproof armour, but still...) I get that you increased the damage from rocket launchers to make up for the fact that they fire more slowly now, but since Cyberdemons don't have that impairment, it makes them considerably more deadly. (and they were already quite deadly!) :P
One thing that i found slightly jarring is the fact that all the things randomly replaced by the mod are re-rolled every time a map is loaded, so when you die and restart the level, you get a completely different set of modifications. The only solution is manually saving on level start, right after the auto-save kicks in. I realize this might be a design choice, made for the sake of variety, but still...
I think the only way around that would be to have it select all the items in a fixed pattern and I don't think that would be an improvement, having everything very predictable. Having it all random, all the time gives it a lot more replay value and makes things a lot more interesting. It forces you to adjust your strategy on the fly and gives a lot more opportunity to see all of the new stuff. :)