I haven't played too much of Fallout 3, but I remember liking two of the companions, the two cities, BoS and Enclave tech, and the idea of project purity.
The companions I liked are Fawkes and Butch, shame because I don't want super mutants on the east coast. Fawkes was just really cool, and Butch was interesting. He's your childhood bully but the first time anything bad happens he cries and asks you to save his mommy, then he mans up and ventures out into the wasteland alone, inspired by your bravery.
I also like Megaton and Rivet City. Moreso the concepts of the locations rather than the locations themselves. A city built out of an old crashed plane with a crater in the center and an active bomb. But why is the nuke there? Why haven't they gotten rid of it? If they saw it there why did they build around it? It would better if the nuke got there afterwards somehow. And Rivet City being built in an old aircraft carrier is a cool idea, although it takes a lot of maintenance to keep one afloat, especially after 200 years of rust and radiation. And the areas inside are really boring.
I wish the BoS and Enclave weren't on the east coast, but the new power armors, robots, weaponry, vehicles, and bases, are just really cool. I like how Bethesda used mind controlled deathclaws instead of intelligent ones, at least I think, I haven't played the DLCs. I really like Liberty Prime, although it doesn't feel BoS. The mobile crawler in broken steel looks very cool. And all of the new power armors look amazing. The flame caster looks pretty cool. And using the Pentagon as a base is a great idea, they didn't do it poorly either.
And Project Purity could've been so cool, but then the BoS Enclave war ruined it. It was mostly to just make the Enclave pose a threat, even though Autumn wanted the same thing as the PP crew. I feel like Project Purity being the main goal for the game as a whole would've been much nicer than having to fight for the BoS.