Fallout 2 lost a lot of that atmosphere "of the unknown" that the first one had. But it gained a lot of technical advantages as well: NPC AI, commanding NPCs to move from doorways, car for storage, etc. Both good games, each with their own faults.
Now that I'm putting some thought into this, I also think what made the first stand out was your primary enemy: super mutants and their leader. At the time, they seemed grotesque abominations, something foreign to the human state bent on taking over the Earth (or at least SE USA). Subsequent games lost that: it has become more of your traditional, hackneyed "you versus some relatable misguided rogue(s)". I don't want to relate to my enemies in a game - I want to be stunned and amazed by their differences.
…so, bring that back, Bethesda (lol, yeah right). Frankly What I want most of all from Fallout4 is the game to delve EARLIER into the history of the vaults. I'm so tired of trying to put myself 200 years post-bombs and still believe half of the stuff that would be more appropriate 10 years afterwards instead.