The technical and balancing improvements are fantastic, much improved (I only played CB's first mod long ago in 2001).
The monsters' immunities, teleporting, firearms, and magic-tech balance are great. It would have been nice if Troika patched these things in 2 years ago to fix the glaring gameplay flaws,
but oh well.
The starting location. The old start wasn't very interesting, but it didn't need to be changed. The new start with the books all over the room and the marijuana zombies is just silly (and opium zombies would have been more 19th century Victorian).
The items you start with. I like the leaf, even though it would be better to be found. It's nice that you're trying to help us out in the beginning, but the plethora of magical items on the player at the start is just nonsensical.
Many of the new cosmetic items just look bad.
Your writing, also, could use some work. Virgil and his friend's dialog are grinding and really ruin the immersion. Your punctuation especially needs work. There are some sentences . They have punctuaction ,like this .
You may also want to go over the backgrounds (even those which are not yours) for technical, gramatical, and format errors. By format, I mean all of the default bg's say something to the effect of 'This resulted in very poor eyesight (-6 Perception)', while many new bg's in the mod are more like 'This caused you to lose 2 points of Endurance'. Some of them have pretty serious errors (one that is supposed to give you +4 in something gives you +10), some are unbalanced and some just suck.
The above mentioned XFiles quest didn't need to be changed. I like how it's bothered me over the years--kind of disalluding (you can kill the big monster threatening the earth, but you can't change the way the world works, and what kind of people run it).
Just a bunch of suggestions...
and it's nice that it's much harder now