I disagree. Better location character and detail, better world cohesion from connections between locations, better writing (on average, boosted by Avellone), better humour.
Location character: To a point, yes, and I always really manage to enjoy most of the game up to leaving NCR without rolling my eyes much at all (though it should be noted I usually save Reno for the late game). Good character doesn't necessarily equate to good in context, though, and the character and detail of locations like Arroyo, New Reno, and San Francisco counts against the game as a cohesive whole for me no matter how much I can find to enjoy in those locations.
World cohesion: I think this is more of a thematic preference than an improvement. In F1, society was still a loose-knit scattering of survivors with wagons circled against the wasteland. Info traveled slowly and was as much hearsay as fact, and even for caravaneers, anything much further than a week's trek was off the edge of the map. I think the islands-of-civilization design principle suited that well and helped evoke a proper sense of desolation and distance, as well as lending additional "mystique" (for want of a better word) to world-spanners like the caravans, the CoC, and your esteemed Vault Dweller himself. Fallout 2's cohesion really solidified the sense of a new frontier civilization, a re-awakened humanity radiating outward from a dozen different wombs and beginning to reconnect, and so the world was certainly
richer than F1's. I wouldn't necessarily say it was better done.
Writing/Humour: As you say, MCA's influence can't be understated, and Black Isle was a stellar team to begin with. I have to factor that against
what they were writing, though, and I've got to disagree on the humour issue so in the end we sort of break even here in my book. F1's writing had its weak spots, but it was mostly great stuff that fit and reinforced the world. F2's writing was phenomenal, but when it's coming from the mouth of a 40's Rip Van Winkle pulp hero, a talking plant, Bruce Lee, or L. Ron Hubbard, I'm less inclined to count that as a point in its favor. Did I laugh more than I did with Fallout 1 the first time I played it? Yeah. Was I also better than half a decade younger than the minimum recommended age? You better believe it. A lot of the humour didn't mature with me though, and it adds more to the nostalgia value than to the game's quality IMO. Even back then, I found stuff like "wish I had a limit break" jarring. P.S.: Every enemy that's uttered a blatantly pop-culture-referencing combat taunt within earshot of my chosen one any time in the last decade has been shot in only the most sensitive parts of their anatomy.
In short, I don't necessarily disagree with you, but most of Fallout 2's (non-engine/UI) improvements are either taste issues rather than qualitative ones or are too well-balanced by rough spots or backsteps in the same departments in order for me to consider them better on the whole. Honestly, I used to feel kind of bad about that, since the F2 team were generally such great, talented people, but listening to the podcast and what MCA has to say about the whole thing, I actually feel more comfortable in that assessment than before.
Edit: After listening to the podcast again, I do want to clarify that the quest design in Fallout 2, as Gnarles Bronson says, does generally show a lot more care, especially where MCA's hand is felt. I wouldn't go nuts and say it was head and shoulders above the first or anything, but it does win out here. At times I feel like some of the quests in 2 get a lot more tedious than the ones in 1, but again, that's a quantity thing: With so many more quests to offer, 2's best is likely to be better and its worst is likely to be worse.