I just played the first two games this year, and I think Fallout 2 was definitely better, even with all the wacky shit and less "grey" bad guys(the Enclave actually felt to me like they were added really late in development, like they'd built most of the rest of the game world and one day someone yelled out "oh shit! We need a villain!").
The sheer amount of content would have been daunting if I'd known how much there was going to be before playing. Sure, it isn't as cohesive as F1, but I found that that gave the game a very different feeling. Where F1 was about a world just starting to get back on its feet, in F2 the world is UP and it's rebuilding itself in all sorts of images, from primitive tribes to slave societies to casino-owning drug dealers, and it's chaos. And they're all infecting each other: NCR is trying to annex Vault City is going after Redding is being torn apart by Jet imported from New Reno is doing business with the Enclave has frightened the Brotherhood of Steel into hiding... the theme of chaos as the world rebuilds itself felt totally intentional, and was pretty much built on in New Vegas, where you help one ideology dominate the whole wasteland.
It sure does have wacky shit in it, but let's not pretend F1 didn't have the Tardis and a crashed alien spaceship with a unique weapon(Mothership Zeta literally would not exist without that encounter, so who is truly to blame?). Plus, for every Hitch-Hiker's Guide reference or ghost quest in F2, there are many more events and moments that could be taken totally seriously. New Reno was pretty crazy, but my enduring memory of it won't be Gangsters & Casinos, it'll be my decision to murder a sick old man for the greater good, or my post-coital talk with Mrs Bishop about how she was seduced and manipulated by her husband, and my genuine horror at the thought of Bishop having a controlling stake in the NCR. Another great memory was the Restoration Patch's addition of the Abbey, where I found out that the magical GECK which was Fallout 3's major McGuffin was actually just a few packets of seeds and a Farming For dummies book. When I realised there was no way I could deal peacefully with the Khans in Vault 15 I felt genuinely sad. And although the Enclave weren't as good a villain faction as the Super Mutants, talking with the president was fantastic. Oh God, and Marcus! A friendly character who also completely believed in the Master's vision was a brilliant idea. new Vegas did a similar thing with the Enclave, which I also loved. I got very attached to Fallout 1's story as well, of course, but I'm mostly concerned here with defending F2 against its reputation for wackiness.
Plus mechanical improvements: the inventory system was better in F2, party members were more controllable. I don't know how different the combat was because I went with a completely different build, but my non-combat build in F2 felt completely viable, and added real weight to the few battles I couldn't avoid (Wanamingoes!
). I don't think I had more than 100 kills in the entire 40+ hours I spent playing. That's a trip to the supermarket in Fallout 3.
Additionally, I played both games fully patched, including unofficial fan patches, and because of this all of Fallout 2's ending slides felt like organic results of the things I'd done in the game(except for the talking deathclaws, but who cares) whereas even with patches F1 has bugged endings for the Followers and the Hub. I know the ending slides aren't the most important thing in the game, but my feeling of agency was hampered by the fact that it was impossible to succeed in certain areas through no fault of my own. Though both games would be on about equal footing without patches, I admit.
And that's one thing Fallout 2 doesn't have: the perfect final ending sequence of the first game. The Vault dweller trudging off into the desert might be my favourite ever ending in a game. The series as a whole has forgotten that magic, of showing you the wider consequences of your actions and then winding the perspective back down to your own personal ending. Fallout 3 tried for that, but Bethesda can't write worth shit. Lonesome Road tried for it, but it's a sideshow that doesn't integrate with the ending of the main game.