It's a Tactics reference. The BoS had a schism over inducting new members, which is why the one group crossed the Rockies in the airships. That alone should have made the Brotherhood of Steel not be present in DC, but Bethesda has face-[censored] a lot of the canon.
Are you sure about that? I don't really remember the Tactics Brotherhood being big on helping people, except as a means to get the people to join the Midwestern Brotherhood. The context of the discussion with Veronica was, IIRC, "So the Brotherhood helps people with their knowledge, right?" "Ha, no. Err... There was one chapter who had a civil war over it though!"
And really, given how the Outcasts and Brotherhood hated each other (there's even a news entry with 3 dog that mentions the outcasts shooting at GNR because it's a Brotherhood outpost, IIRC), I could easily see them having a civil war.
On further thought, though, I can see that it does fit the Tactics Brotherhood as well, I suppose.
They fight in Fallout 3 because 1) Bethesda lacked the imagination to create their own factions and put their own stamp on the brand, simply re-using and ruining the ideas of the first games and 2) Emil can't write.
*Nods sagely.*
Though, and I feel somewhat dirty for saying this as someone who played the originals before FO3, I could sorta see why Lyons would start helping people out of the goodness of his heart. He was a veteran of the scourge of the Pitt, which was apparently pretty damn nasty before the Brotherhood purged the place. Casdin grew harder and colder, while Lyons started sympathizing with wastelanders, and over time (and seeing how completely pathetic the capital wasteland is to the thriving societies he's used to), he probably would have started going native.
Lyons was one of the few halfway decently written characters in the game, if not the only one... And even the weakest character in NV blows his writing out of the water.
Edit:
Seriously? I don't hear people complaining about the lack of Enclave encounters in NV. Nor I hear complaining about the new factions.
In the DLC suggestion threads, it seems like we can't go a day without some person coming in and saying "Enclave Invasion DLC!"
That and "Freeplay after the end!"
Don't those people realize how
lame Freeplay is after you've already seen the ending slides? I mean, the only reason to play on in FO2 was to do lulzy stuff like abuse the hintbook and listen to the druggies talk about how you blew up the Enclave.