Isn't the difference that FO1 had lame nerd culture Easter Eggs, whereas FO2 had lame pop culture critical path elements? Like the main antagonist being a Secret Service agent named after the protagonist of In the Line of Fire? And the nerd culture vs. pop culture thing is non-trivial. I'm not a Dr. Who guy, but the Dr. Who reference is a shibboleth so that the designer and player can identify each other as the same tribe. I would say that is arguably even true of South Park in 1997 (its first season). By contrast, a lot of the stuff in FO2 is just pop culture stuff that sometimes felt a little like a behind-the-times uncle -- Dan Quayle jokes in 1998, six years after Quayle had been out of office? Mike Tyson biting Evander Holyfield's ear? As Good as It Gets?
Also, I would say the problem is actually less with that kind of small stuff, and more with whole areas being seemingly out of theme, like the Temple of Trials (though I've defended its aesthetic elsewhere), Yakuza vs. Scientologists in San Francisco, etc. And even off the critical path, it's not like this stuff is weird outlier material, it's everywhere you go. I mean, I've often made fun of Pirates of Darkwater, a cartoon I loved, by having not one but multiple "heroes must rescue a cute animal" episodes; FO2's comparable thing is not one "lol, it's an animal but it has human intelligence" encounter but three (? four? I can't remember -- there's Pinky and the Brain, the scorpion, the Death Claw...). Overall, FO2 felt more like Wasteland's setting in some ways than FO1's in terms of the zaniness level.