Personally, I think that the faction of the Enclave in Fallout 3, should be considered non-canon, as it seems to move away from being The US Government, which is attempting to restore "Pre-war America", to clownish "super-villains", led by a computer, and commanded by a man in a trench coat. Before you know it, Colonel Autumn will reference everything with the words Gestapo in it, and he'll be given a short assistant named Von Smallhausen.
But the Enclave in Fallout 3 IS canon because they are a natural progression of the Enclave we saw in Fallout 2. Of course they care less about restoring the US and being the US Government (its only Eden really who talks that way).. their true leadership was destroyed.. If anything I think the changes we see are a natural progression of their society. I dont think Id call them super-villains any more in Fallout 3 than in 2 either, if anything they are less menacing in Fallout 3 than in 2. Really they are just a bunch of raiders who inherited a high-tech legacy and whose purpose seems to be maintaining the status quo of the Enclave. In Fallout 2 they are narrow minded towards a fanatical purpose. THEY are America and all others are not. It is their duty to cleanse the wasteland to prepare it for the second coming of the United States. In Fallout 3 it seems that Eden is the only one who still believes that..
Consider that the true Enclave is gone, those who are left were not as high up the ladder authority wise, and a generation after the destruction of the rig probably care more about ruling what is left of America rather than rebuilding it, and the United States is just a shadow from history and not the future. A good example is Autumn, who despite the fanaticism of his father in following 'President' Eden to the East Coast, isnt as fanatical towards the Enclaves original purpose. Autumn was more interested in using the clean water as a method of controlling the wasteland to the authority of the Enclave.
Having a small assistant named 'Von Smallhausen' isnt as clownish to me as having a Vice President named 'Daniel Bird' or a military commander named 'Colonel Sanders'.