I haven't beaten it yet, but agree that it feels dated in many ways and even a step back in some. The questing and exploration are especially not fun most of the time. The number of loading screens and amount of fast travel are obscene. I find the dialogue so tedious that I skip the majority of it and even sometimes don't read the options that I'm choosing because it rarely matters what I choose. Like you, I noticed that how I carry out quests also rarely matters. I had a similar UC quest in which I was forbidden to kill anyone, but I killed literally everyone, instead, and my commander was livid... for a minute... then he was back to praising me and giving me my next assignment. Also, last night, I was asked to choose whether to free something, but it ended up getting free no matter which you chose. Finally, lots of little things are getting on my nerves, like waiting for characters to stop talking before I can even engage them in dialogue. Last night, I had to wait several minutes while a married couple talked about their marriage, with me standing right there, so that I could talk to one of them and get on with my important mission.
That said, I'm still occasionally enjoying it (usually the rare times when I actually get to shoot something) and I'm still playing it after 4 weeks, so there's enough to come back to, but I think that it's my least favorite Bethesda RPG. In fact, I was reading the other day that it's Bethesda's lowest rated on Steam. It's still at an OK 75% positive, but lower than all of their previous RPGs, even the maligned Fallout 76, though only by a hair.