I don't see what the problem with BoS and the Enclave being in Fallout 3 is. Correct me if i'm wrong, but The Enclave was the "Shadow Government" of the United States before the war? Wouldn't it make sense for them to have presence in close proximity of the capital?
As for BoS, yes it seems a bit silly to send a chapter all the way across country to retrieve technology, but not complelety implausible (IMO) either.
What I think is a bit silly is that in Fallout 1 you meet the BoS, who is a minor faction, isolationists, xenophobic and they're not that many. Then you see the super mutant army, who are created from FEV which only exists in Mariposa, and you kill them off and the remnants scatter and flee in different directions to the east. In Fallout 2, there's the Enclave, who has their main base and most personel at the Oil Rig which you blow up and therefore the Enclave is pretty much dead.
So, we have the minor faction BoS which is declining and are probably inbreeding. We have the mutant army, who can't reproduce without kidnapping humans and dip into FEV-vats which only exist at Mariposa which they've now fled and they've scattered. We have the Enclave, who blew up and what remained at Navarro and their refuiling depots probably scattered aswell, like told in NV, they tried to integrate into the NCR but was hunted down for their past, so they have to flee and hide their identity.
Then, in Fallout 3, the BoS shows up in a bigger force than they ever were in Fallout 1 and 2, and this is apparently just a fraction they sent, across ~3000 miles of post-apocalyptica to convenietly get to the same city where there's a HUGE army of Enclave, which were terminated in the last game, and also a HUGE army of super mutants without a leader, and they apparently come from a Vault that somehow had FEV, which they in the game seem to have run out of, but there's still tons and tons of them how many you kill and there's no way to liberate the wasteland of them.
In conclusion, three major faction in previous Fallouts who are either dead, scattered or declining, show up in HUGE quantities in the same city ~3000 miles away.
It's basically these plotholes.