Yes, this is what Fallout 2’s main quest should’ve have been! Fallout 2 sets up this really interesting geopolitical landscape and gradually reveals how the enclave is worming it’s way into this power structure (trading with the Salvatores) and then... none of that matters, the Enclave want to release a super virus to kill literally everyone else on the planet and only you can stop them.
I mean debateably, the Enclave's actions in the Wasteland were all working towards the modified FEV. They got Chemicals from the Salvatores to work on it, they mined the FEV over in Mariposa, and bought and captured slaves to work on the FEV, they kidnapped Tribals and Vault Dwellers alike. I think the entire way the Enclave interact with the main plot is written around the assumption they use FEV.
But I also agree that there is something dissapointing about the Enclave's end goals.
People on this forum will often talk about having negative experiences of the end-game, and will often attribute it to San Fransisco, but honestly, I think San Fransisco gets a lot of shit for flaws which ultimately come down to the Enclave being a massive dissapointment. It's fine to have unambigously evil villains, I didn't personally mind the sillyness in most characters being contemporary 90s Clinton Impeachment references, and Frank Horrigan and President Richardson were pretty compelling characters.
The problem is that Fallout 2 has spent it's entire main story creating a complex world with a functional economy, and a genuine focus on material scarcity and how even seemingly minor objects have vast implications for dealing with this economic scarcity (You start off repairing a Distillery in Klamath so the local bar can afford to undercut alcohol prices, since most of the Wasteland's alcohol is mass-produced by the Wright Family, later in the game developing a cure for Jet addiction means handing over power to a fascist state, and recovering an advanced piece of mining equipment from a recently destroyed mine can literally shift the balance of power in the entire wasteland)
What makes Fallout 2 great is that the material scarcity of this world means that they don't need incredibly over the top stakes. Literally controlling a tiny piece of advanced, hard-to develop technology can permanently change who holds power in that economy.
Then final act in the game comes and: you have an entire faction able to create technology that outright surpasses that of the old world while solely using whatever shit they can salvage from a single decaying oil rig, and their entire plan is literally so high-stakes, so impossibly huge in magnitude that it effectively amounts to "We're literally going to wipe out all life on earth". And the jump from "This one tiny piece of ancient mining technology decides which mine becomes more succesful, which will decide who controls the flow of gold and therefore who ultimately controls the economic sphere of Northern California" to "We literally have the ability to mass-produce higher quality technology than the brightest minds of the pre-war United States, and are using that to literally kill every single character you've met in the game in an instant" feels like a jump that's never justified, and feels like a jarring addition to a game that despite it's silliness, was actually incredibly deliberate in what it included.
I mean it didn't have to be this shit: the game takes a lot of care explaining how the Enclave acquired the FEV, how they acquired the chemicals to modify the FEV, how they got the test subjects for their project, and how they utilised multiple sources of Slaves both from trading with the Slaver's Guild, and striaght up kidnapping them from Redding. And for the most part their impact on the gameworld was actually that cross between small stakes but big consequences: the fact that the Salvatore's are acquiring Laser Weapons is both a minor point, and literally their entire plot to take over New Reno. The way the Enclave are set up is consistent with the rest of the game, and could have leant itself easily for a much smaller-scale, much more logistically sensible version of their current plan. The Intrigue is set up fantastically.
But then at the last act of the game it feels like a rushed Doctor Who plot point(Don't know if the originals are like this, I'm a casual and only watched nu-Doctor Who), where after having all this intrigue and excellently built suspense, the writers suddenly decided "Hey, this concise intrigue based plot isn't significant enough, let's drop everything and make the bad guys have a secret plot whereby the entire world is at stake literally unfolding right now", and just overlooked the entire logistics of how it works, throws in the most high-tech faction seen in the game so far with practically zero of the scarcity seen in other high-tech areas like Vault City, and decides "Hey, the entire world is at risk if you don't hurry", and that's just it, game over, have fun everyone.
And because the stakes are too big to comprehend, and the logistics don't make sense, you have to switch off your brain, and suddenly there's no tension any more. Everything is so impossibly yet unjustifiably grand, that you don't appreciate what's actually at stake here. If there's literally a Dalek coming out of a fucking ark ship every single second, you don't appreciat the power of a Dalek. If there's literally an Oil Rig with the ability to end all life on earth, you don't really appreciate the actual consequences of their plot, because it has no consequences, it's literally there to be the highest-stake plot imaginable.
Like, I'd love to see a version of Fallout 2 where the final encounter with the Enclave, these villains the game has been building up to so much, didn't feel like a rushed, over-the-top array of plot contrivances that take away from what was otherwise a pretty awesome and well-thought out game.