Genetically inferior in what way? I doubt it's anything that couldn't be fixed (or even needed to be fixed). We have some amount of genetic engineering even today, with Fallout technology I can imagine them being able to alter genetics in any number of way. The wastelanders might be genetically superior in some ways. Ghouls, as deformed as they are, have much longer lifespans.
As for Mr. House, for him to stay alive he would need extensive knowledge of human biology, medicine, and genetics. His medical technology is far beyond what even the Enclave has, and yet he finds no problem with the post-war humans that he's been surrounded by for 200 years. It seems much more likely that the Enclave was simply wrong, or they overreacted to biological problems that are minor at best.
Well for example, the people from Vault City who have been experiencing radioactive contamination via water polluted from a nearby powerstation, everyone in Vault City now suffers from fertility problems and people are born with chromosal damage and Vault City had the finest medical technology in California, just like in real life, radiation in Fallout can cause realistic birth defects and mutations as seen here. Even decades after Chernobyl people are still been born with them and a similar situation will have happened in the Fallout universe where the contempory wastelanders still carry genetic abnormalities from the original generation during the war. House's machine could do any number of things, I doubt that he personally built it. Besides House worked with the Enclave before the war and turned REPCONN into an energy weapons manufacturer for them, REPCONN built those plasma rifles after House's takeover. Gannon says, "I've read about REPCONN, they did some work for the...... for the government before the war." Obvisouly covering up the fact that he was a member of the Enclave, take him yourself to the REPCONN headquarters. If House had it then I think it's pretty much certain that the Enclave would no, the Big Empty , according to Elijah, has hibernation chambers, statis pods, whatever you want to call them which I would imagine work in a similar if not better way than House's machine which was designed to keep him alive but also via that headset thing in constant connection to all the computer systems in the Lucky 38. Statis chambers are not unique to House and if a highly advanced pre-war, inhuman laboratory like the Big Empty was building them it's pretty much certain that the Enclave must have been involved or surely know. The Enclave are not wrong, their entire virus plot needed to be tested on pure-human stock from Vault 13 and the freshly mutated people from Arroyo, the pure-humans experienced much longer and more excruciating deaths than the mutants.
Right after the war there was no NCR, and no raiders or tribals. There was just a bunch of frightened people looking for some kind of stability or safety. In a disaster (especially one of this scale) it is the obligation of the government to provide support. Everyone in the United States directly after the war would have followed the orders of someone claiming to be the government, they would have no reason not to. The purpose of a continuation of government is to continue government. If the Enclave doesn't even try this at all then they lose their claim to being the government. Groups like the NCR were made out of necessity, because the old government abandoned them.
Actually there were lootings, mass hysteria and a complete breakdown in society if that Ghoul in Underworld is too be believed along with infernoes which burned for days. The Enclave was not technically the government and it all depends on what you envisaged them doing before the war, the Enclave was a secret cabal of power brokers, military leaders, politicians, media and such who usurped their positions in some kind of common agenda; when it became aparent that nuclear war was approaching, the Enclave decided that it would use all it's power to ensure that the government survived after the war. What could have happened was maybe the President was a member, or the Vice-President whatever, after the war they still have authority and if the President died during the war then the Vice-President would become President until time came to hold elections, through someway which may even have involved re-writing the constituation (or maybe they official acknowledge that the mainland is no longer America?), the wastelanders are not American citizens as can be observed from the Fallout 2 Enclave Patrolman dialough,
"You are an enemy alien". The Enclave now are the decendants of the pre-war Enclave.
There was no centrilised authority after the bombs fell, the Enclave isn't respomsible for every police, fire service etc. for example the German Town Police department tried to help people on there own because there was no communication from anyone, even non-Enclave government, they had a refugee camp for a while till everyone died of radiation posioning. Still what is your point? The Enclave retreated to where-ever and when they decided it was time to see if everything had settled sometime in 2170's they saw a lot of [censored] in California and decided "[censored] it" basically, the situation was irrideemable. The fact is they waited too long on the Rig and things slid beyond what they had any realistic power to control.
How far would the range of the poison be though? Even if they could kill everyone in the former US (which is doubtful) they'd be leaving the new US incredibly weak. Other countries would eventually want to see what happened to the US, and (while they would be hurting from the war as well) they would find the new US to be nearly uninhabited. Eventually people would try to repopulate it, and the relatively small Enclave would be swept aside and destroyed. They may even actively hunt them down after what they did. The poison plan would only work if it killed almost everyone in the world, which would be impossible. Also, while the current Enclave generation would agree with the plan, eventually their descendants would be horrified at what happened, and the government would most likely be overthrown.
It was a virus and the range was global, the President explains it, it will be relised into the http://en.wikipedia.org/wiki/Jet_stream which will carry the virus just like radiactive fallout itself around the globe and kill all those who contract it. Other countries are in no state to come en masse to the US and pick a fight and if the Enclave is as powerful and commanding as you say then surely any remnants of the American people which survived (though none would as previously stated) would keel beneath the Enclave's military superiority. Why would the decendants afterwards rebel over a genocide which was in the past, what would they overthrow and why? They overthrow the then contempory government over actions in the past even though the then government would also be comprised of people who weren't even alive during the actual genocide.
Besides they planned for near global genocide, this isn't F3 with the water plan, the virus is airborne and will be carried by currents across the world, viruses can survive extended trips on the sides of satilites so I can only assume that the Enclave engineered the virus to be able to survive the extreme conditions of being swept around the globe.