Fallout 3 was a more evocative game for me (artificial green filter aside). It really captured the the bleak, merciless nature of the wasteland while portrayed a kind of lost wonder to the once-mighty nation that came before. You got the sense that this world had indeed lost something immense all those years ago. It did make it a little depressing to play after a while, but I can still admire it in that respect.
In comparison, Fallout 4 is a lot more colourful, lighter, and vibrant than before. In a way, this allows it to be more expressive with its art style and provide some much-needed contrast that was lacking in previous games. This is particularly effective in the glowing sea, which feels much more like a kind of forbidden no-man's land with the widespread radiation and difficult enemies than even the harshest parts of Fallout 3. I hate it, but that's what I love about it, if you catch my meaning (bit like the Dwemer ruins in the Elder Scrolls games).
But there's something that puts me off about Fallout 4's atmosphere. It's hard to explain, but it almost feels a little too busy. The world map is crammed with locations, but they all feel a bit too close to one another. There's seldom a moment where something isn't happening: that's great from a gameplay perspective of having something to do, but I kind of miss my long treks in the scorched landscape of the Capital Wasteland. I miss that sense of journey in previous games.
That doesn't make Fallout 4 a bad game, of course (in some ways it's far ahead of 3 and New Vegas), but it does feel like it's missing something.