Like:
The new perks. In particular, Sneering Imperialist. Granted it only has a couple of dialog options, but it fits so well for many of my characters. And it applies to most of the human enemies I go out of my way to kill as well! Fiends, Khans, junkies, tribals... Too bad it doesn't count Legion, but I can understand why it doesn't.
The survivalist and everything connected to him. His story was heartwarming and evocative and was a true masterpiece of video game writing. Especially his final note with the gun and the explanation for how the Sorrows got their name.
The landscape of Zion. I know how atrocious the gamebyro engine is for this, but somehow Obsidian was able to work around this to make an extremely breathtaking vista.
Weather. I've used mods for this for ages now, but it's real nice to see it actually happen in an official product.
The characterization of Graham and Salts-The-Earth. Graham in particular was one of the most interesting and deep characters in any Fallout game. I also liked Follows-Chalk's characterization very much.
The Colt M1911. Screw the Thompson, the Colt is one sixy gun. I don't like the unique one so much because it's not as huge, but still. I wish it had an extended mag mod though.

I really liked the atmosphere. Despite my general loathing for tribals in Fallout, I got a good sense of how these tribals came to degenerate from prewar Americans, and the atmosphere of Zion was a huge contributor to this. It really did feel like somewhere tribals could exist without being exterminated by someone more organized like NCR.
Dislike:
I thought the Caravaneers were somewhat underutilized. I'd have liked to see more of them.
Getting around kind of got tedious in the end. I think they could have done with a few more access points to the various cliffs.
Daniel didn't have as much character development as Joshua did.
I could've used a bit more non-tribal loot. Maybe another E-weap, and another suit of non-tribal armor would've been nice.
Those creepy rock paintings with the people who are really tall and have tentacles for hands. Every time it got dark out (esp when it rained), I expected the slender men/skinwalkers to come out and attack me. It was somewhat disappointing that they never did.