It's bullshit that you can't talk down the Enclave in Fallout 2 the same way you could do to the Master in Fallout 1. At least you can convince Richard Grey that he's wrong before he blows his own brains out. And unlike Fallout 3, where the Enclave knows who you are and knows to shoot you at first glance, in Fallout 2, you can infiltrate them, down to the point where everyone from their president to random comm officers and drill chiefs believe you to be one of them. So why not go the extra mile and have a very persuasive Chosen One smooth-talk the Enclave into joining the NCR and dropping their genocidal bullshit plans?
Especially when you consider that 1000 idiots in an oil rig and a couple hundred from a military base will wind up dying out due to inbreeding in a couple generations. Meanwhile, if they intermingled with the mutated humans and used their firepower to restore order and civilization to the wasteland, they not only could get more resistance to the harsh conditions of the wasteland, but also gain a larger pool of manpower for workers and cannon fodder. The Chosen One can use that to convince President Richardson that making peace with the NCR is a far better option than allowing less than 2000 people to inherit the Earth and eventually die out from inbreeding.
Sure, have the ending where you blow up the Enclave and feel like a badass, but would it kill them to have an ending where the Chosen One, having seamlessly infiltrated the Enclave, persuades its leaders to make peace with the NCR instead of committing genocide? It would have been a lot smarter and it would go a long way to explain how the NCR suddenly became Imperialistic in New Vegas and how they defeated the Brotherhood of Steel. The NCR becoming imperialists and them defeating the Brotherhood would make far more sense, if they have American government remnants lending them power-armored soldiers to make short work of the Brotherhood of Steel while trying to get them to retake as much of old America as possible.
Suddenly, the NCR going from democracy to imperialism would make more sense, especially if the Enclave joined them and convinced them that they rightfully own everything from California to New England. You can even explain away the Fallout 3 BoS and Enclave by saying that the BoS in Fallout 3 is what's left of the Brotherhood, fleeing to the Capital Wasteland from the west coast after the NCR and the Enclave tried to eradicate them, and the Enclave in the Capital Wasteland was a detachment of troops sent by NCR/Enclave leaders back in the west coast, whose goal is to finish the eradication of the Brotherhood and establish a base at the nation's former capital.
For the Enclave shooting Vault 13's dwellers, I'd assume the ones at the door would be excused as "compromised from background radiation" along with the fact they could use any other excuse like "the Vault Dweller brought in radiation and dealings with the BOS for some computer that replaced the Overseer." Plus there's the FEV. They needed some lab rats and the dwellers of Vault 13 was their best stock for part of an experiment. At the very least with the Enclave of Fallout 2, they weren't being led by a Southern accented man who sounded like a cuck when he tried to assert himself with "I AM IN CONTROL HERE, I AM THE ENCLAVE" and they had more power back then compared to whatever they had in 3. One could assume the Enclave of 2 had enough citizens to make the society they wanted and if any vault that wasn't part of some experiment survived, they'd likely hunt down those vaults, recruit the populace, and give them a bogus story of what was going on in the outside world after the bombs fell. Meanwhile in 3, Autumn's plans were going in a different direction in not wanting to use the FEV since he may of not been as genocidal as Dick Richardson.
As for Eden, it's been years since I played 3 but I thought his reasoning boiled down to "reading every info and order behind a president and emulating their actions." In his case, I'd imagine Eden wanted to make use of the FEV to live up to some part of Richardson's legacy. Eden was more or less an AI or computer that was running on exceptional programming. Meanwhile, Autumn at least tried something different. As for firepower and the Enclave in 2, I imagine using the FEV would save them manpower, time, and bullets. Why waste a bullet or energy cell on a bunch of tribals and wastelanders when the science teams cook up a new deadly gas that'll spread around the airstream that'll kill everyone that hasn't gotten their vaccinations.
That's the problem, though. They had more power. The FEV plan was completely unnecessary. Not just that, but the Enclave in FO2 consisted of 1000 yahoos in an oil rig and maybe a couple hundred in the nearby Navarro base. If they used the FEV and killed damn near everyone, they themselves would die out in a few generations due to inbreeding and living in a still-irradiated environment. In fact, MATING with the somewhat mutated wastelanders would probably make them more resistant to radiation, since the wastelanders would naturally have built up a stronger resistance to radiation when compared to people hiding in vaults and oil rigs that for all intents and purposes, are akin to the Quarians of Mass Effect: safe inside their own environments, but if they go outside into the irradiated wasteland, the radiation and elements will hit them full force. Not only does the Enclave in Fallout 2 come off as needlessly brutal, but they're bigger idiots than Autumn ever was. Augustus Autumn at least realized his Enclave government will need the support of wastelanders to survive, so he wants to seize a local water supply and use that as a bargaining chip. That, and Eden's plan to kill the mutated wastelanders is something born out of desperation: both his Enclave and the Brotherhood can't stop the city's mutant infestation, so instead of fighting it block-by-block like the Brotherhood does, he instead opted to start with a clean slate. Sure, it will kill some innocents, but it will clear the way for the pure humans of the Enclave to take the city with minimal resistance.
Actually that gives me something to think about. Eden would have been built by the original Enclave while Colonel Autumn was a descendent of them. In fact Colonel Autumn would have been from the military side of the Enclave, possibly descending from US military personnel. Richardson would have been many generations down from the original Enclave but acts just as genocidal as the original. Perhaps there is a schism in the Enclave both generational and between the military and political class. The military, being the descendants of veterans who bought into nationalistic propaganda and fought for the American people, would have wanted to protect them. Something like a benevolent dictatorship. While the politicians were selfish and viewed the rest of humanity as inferiors to be used in experiments.
I suppose that's what sets apart the Enclave commoners from the political elite. The top brass see people as expendable buffoons to be used for science experiments, while the common soldier just wants to bring order. FO2 was strict in its idea of the Enclave as a genocidal government body, but FO3 and New Vegas established that the Enclave just wanted to bring back some semblance of order and didn't think the wastelanders can do it on their own. It seems that FO2's events killed off the Enclave's political elite, leaving only the military class that wanted order and peace, which is why the FO3 Enclave is a more nuanced adversary than the FO2 Enclave, and the New Vegas Enclave is downright pitiable and sympathetic at the same time.
To be fair about House's elite arrogance, he's, possibly moreso than anyone else in Fallout, earned it. If I shot down the majority of the nukes headed for an entire region after calculating events to within a day's margin of error, I'd be pretty arrogant about it too.
He definitely has some flaws, unaware of the darker side of the White Gloves for one, and the Omertas for another. I suppose with the Omertas he had them play into his nostalgia for the mob with the reasoning that it was better to consolidate a black market that was always going to happen into one major player. Still doesn't work out well without the Courier's help. To be honest, the thing about him that pissed me off the most was destroying the Kings if you broker peace between them and NCR.
Otherwise, though, he doesn't like to stray from his plans but he will absolutely do so if it's merited. Picking Courier Six as his new agent, the factions you can convince him to leave alone, etc. Hell, the Brotherhood he ends up being right on refusing to compromise about.
Yeah, he's apathetic to the plight of everywhere that isn't his personal fiefdom, but he's pretty open and honest about that, you can still help those places as well, and I find it sort of amusing that the best Wild Card endings (in my personal opinion) are mostly the things he wanted done with/to factions anyway.
So, like every faction. He's got his bad, got his good. I'd say he's the best option.
I'm pretty sure if I averted apocalypse and revived my own slice of America after the bombs dropped, I'd be arrogant as fuck, too.
I attribute his inability to gauge the Courier and the White Gloves/Omertas to the fact that he always looks at the bigger picture more so than the little guy. When it comes to small details like the loyalty of some tribes or the loyalty of a Courier, he's not able to read things accurately, assuming they will simply serve because they signed something or agreed to serve. But when it comes to dealing with the Legion and the NCR, he's practically playing both for fools.
As for the Kings, on a House playthrough, I always turn them against the NCR, while in a Yes Man/NCR playthrough, I get them to always make peace with the NCR.
The Brotherhood is not a stable faction. It's too powerful to be ignored, but too erratic to be trusted. The NCR found that out the hard way when the West Coast Brotherhood went from ally to enemy and declared war on them for daring to try and use Enclave tech, whereas the East Coast Brotherhood went from a local security force to a bunch of zealots going on a fatwa against all synths.
House is, at least, a known quality you can deal with honestly. He's a dictator you can do business with. He's not as inept as the NCR, not as brutal as Caesar's Legion, not as erratic as the Brotherhood of Steel, he's someone whose agenda is well-known and can be dealt with accordingly, on cordial terms. So long as you don't fuck with him, he doesn't fuck with you, and loyal service is always rewarded.
All the Mojave Factions are screwed one way or another, House is just the least screwed out of all of them.