I already said and reaffirm that I actually quite like it. It makes perfect sense from a story perspective where it ended. They have professional writers doing it and it shows. Getting there was a bit silly
If I had control of the story I would have created a stealth mission instead where you basically need to sneak in and hack a system through the walls and ducts etc... it would make more sense. Imagine hacking into the system and then you could have alarms and the bots chasing around through the ducts. Needing EMPs to disable bots before they can raise the alarm. I would make it so that if you went the way you go in the game you just get overwhelmed unless you are superb and have basically full ammo on every single gun.
However I missed out on getting to really use the BFG much as well. Also as I said the textures were super jarring and repetitive there. If you did the sneak thing it could be like portal's hidden rooms with graffiti and stuff from prior people. Also no boss fight actually makes some sense. You aren't going to keep a raging giant mutant in the capital