Two was already on the path of forgetting them. The theme of fallout does not need them, they are just the results of that theme: that humanity can survive, and rebuild, and they'll try to rebuild in different ways. That theme could manifest in a lot of different ways.
Given the nature of the world in Fallout, any large scale organisation such as the Brotherhood of Steel or the Enclave wouldn't necessarily collapse with the loss of one branch. Its probably easier to describe them as cells rather than a single entity. Yes, the Enclave leadership was killed on that Oil rig in 2, but considering that the Enclave was the remnants of the US Government, there would be multiple sites and plans in place before and after the bombs dropped, one needs to only look at the US Continuity of Operations Plan to get an idea of how extensive it is. Likewise with the Brotherhood of Steel, given the number of Army bases and bunkers that exist in the States. All of them would be connected by some sort of network, government and army alike.
Ultimately it is easier to kill an man than an idea. An idea can be a wondrous thing; such as clean water in the DC Wasteland or rights for synths in the Commonwealth. But it can also be a dangerous rallying point; Ceasar's Legion, purifying the DC Wasteland and so many other evils.
But the theme of the Fallout games? Its not about humanity rebuilding. It hasn't, not really. People scavenge, they loot and they patch up what they can and if they can't, they steal from those who can. But there is nothing new, no real growth and development. One can see the true theme of Fallout is about the inherent flaw in humanity where we can't let go of the past and seemingly unable to learn from our mistakes.
Examples:
*The Brotherhood of Steel in the West and Mojave are almost extinct due to unable to appreciate the idea that they don't know everything, because they constantly underestimate wastelanders or anyone not a member of their organisation. Conversely, the Eastern Brotherhood under Lyons flourished because they were more open. Under Maxson, they have become feudal lords, but potentially decimated in several endings. A major reason why the Western Brotherhood Chapters are failing is because they cannot appreciate that for all their hoarding of technology, people don't really need a laser or power armour to beat them. They suffered massive casualties against the NCR, even though the NCR still use police level gear with rifles, but that's all backed up by numbers, artillery and aircraft. At the end of the day, they seem incapable of learning from the past.
*The Enclave cling so desperately to the idea of the US of the past that they cannot see the population of the post-War landscape as anything less than human, despite say Ghouls actually being people who actually lived in the US. They are so intent on "rebuilding" the old world that they are prepared to commit genocide. Yet, some might see their actions as the same that led to the destruction of the Old World.
*Ulysses throughout New Vegas, like the Enclave, cannot let go of the concept of the Old World. Ulysses cannot let go of the past, from his coat and signature weapon, to the rage he felt at the White Legs copying his old tribe's use of dreadlocks. Consider the question that he asked the Think Tank - "Who are you, that you do not know your own history?" and the chaos that caused. If you choose the right options when you confront him, you basically throw the question back at him by forcing him to realise that his actions caused the crises of Honest Hearts, Old World Blues, Dead Money as well as the main story, all because he wants to bring the old world back.
Ultimately, Fallout believes that people can't let go, be it the past or an idea and more often than not, the protagonists of Fallout are not so much the ones who are best at surviving, but rather the ones who make the sacrifice to look to the future.
Rose of Sharon Cassidy's last words in the House ending probably best sums it up: "We were going full speed ahead...but facing backwards the whole time."
At least that's what I think...