I experienced this same thing with a challenging Bank Headquarters run last night...
Took forever to kill any NPC and just felt way more difficult that it was pre patch.
I don't know what is going on, but I suspect them nerfing damage via check piece talents and DTE has had a very negative effect on TTK which makes the harder difficult very frustrating.
We seem to be in a vicious cycle with this game...
It became harder but still soloable. I've made a video soloing it in 25 minutes withouth deaths (but still I've been knocked down for three times), but I don't think I should upload it since I didn't check the microphone settings (I'm bearly heard), besides there are some lag spikes, 'cause my CPU can't handle smooth encoding (think I gotta lower the resolution of the video or overclock the CPU). But if you want me to I can upload the vid. x)
For me it's harder. Because the patch ruined my build completely. I had a tanky/dps build in which I could faceroll challenge missions without using any covers (actually I used them, but just for reloads) just by running towards my enemies and outhealing all the incoming dmg, balancing at 50-100% HP (thx to clutch+safeguard talents). I was smth like 5 offensive stats and kinda like 10 defensive ones, it was about 130k HP and 215k armor. At 0 armor I was becoming a MONSTER because of berserk + straind talents, which were both nerfed by half in the patch. I had ~110k crits with AR at 38% crit chance rate and smth like ~80k crits with SMG at 52% crit chance rate). But thx to the 'awesome' patch I'm neither takny anymore, nor pew-pew. Now I have 50% crit chance with AR and capped with SMG (60%) but the dmg is incredibly low despite the fact that now I have 9 stats in offence. Now my crits are smth like ~65k with AR and 52k with SMG and I'm at 110k HP and 185k armor.
I can't remember the last time I did this mission, but I could just not complete it today on challenge difficulty, and I had to reset to hard.
I'm currently getting through most other missions on challenge, without being completely inundadated by 4-5 waves of enemies and 2-3 warhounds at once, etc. I considered switching to the pulse skill that disables electronics, but honestly, even that probably would not have helped. Every wave of enemies had one medic in it, sometimes yellow elite, and I often couldn't kill him before he started rezzing everything around me.
I don't know if it's just this particular mission, but it seems way out of line with the rest.