The Captain Hunter fight was a little irritating/kinda impossible. The pulse grenades you find earlier didn't take his shield down (although they dealt with the bots upstairs) and the shield console was positioned such that it wasn't feasible to turn it off when he could one-shot/two-shot you on the way to it. Hiding behind cover and wearing him down with flame weapons that ignore shields wasn't possible as he'd just run out and gauss you in the face- in the end I had to kill him through the console.
The 'walk into room, somebody oneshots you' problem did crop up a few times- Captain Hunter, Jeb, and the Legionaries with hunting rifles all start combat with you in front of a doorway, at near point-blank range, and all have high single-shot damage weapons. The end result is a lot of reloading. Maybe adding some cover to these encounters would help? Or at least a degree of delay when starting. One thing to note from the Fallout 3 maps in particular is almost every map with hostile NPCs has an 'antechamber' just the other side of the load door, in which you're safe- allowing you to play around with going into fights with different weapons equipped and different chems popped without having to save before the load door, then cell change, then reload.

Conversely, the fights with the prospectors with assault rifles were almost trivial- they all had high ROF/low DAM weapons and couldn't beat Combat Armour, Reinforced- admittedly I was using a 'minimum 0% damage' mod but I can't see them being much of a thread with higher minimum damage either. Peppering in a few hunting rifles into their loadout (and a few ARs into the Legion loadout) would help level out the threat each side posed.

The only other things I'd note would be the lack of a doctor- so on hardcoe, broken limbs are gone for good. There's a profusion of medical equipment around, but not the right bits to build doctors bags, sprinkling in some Surgical Tubing, Forceps and Scalpels amongst the Blood Packs would fix that.

Oh, and there was a missing texture on the tunnel entrances.