It isn't that people are making the case that Lyon's Brotherhood and the Enclave being in Fallout 3 is in anyway canon breaking. It's more the argument that Bethesda should have come up with original factions and come up with an original story line for Fallout 3. That gets us into debates about which Fallout is better and such and I can see how it is seen as people just crapping on Bethesda.
There's also debates about Lyons being a competent leader or not and if is actions screwed the group over.
Now Super Mutants being in Fallout 3 will spark debates about canon and whether their being there or not goes against canon. But that's another matter and at this point in the forums here I am sure people are tired of that debate and just except that they are in the game. I am inclined to agree.
The issue I've found for most people is not how Lyons is portrayed in relation to the BOS, since its made very clear his actions aren't approved by the rest of the Brotherhood leadership. And we have an entire faction (the Outcasts) to show how the Brotherhood is supposed to act.
People normally hate Lyon's BOS because 1. Horrible writing of the storyline and 2. the fact that we are railroaded into following them. To the point where there is literally no option but to support them.
Kill off everyone non-essential in the Citadel? Nope. Still gotta serve them.
Decide to side with Eden? Nope. Turns out the virus svcks, gotta get back to ol' man Lyons.
Want to do anything but work with Sarah and her daddy for the main questline? Screw you pal, get back to serving the Brotherhood.
Its annoying, and ham-fisted.
Annoying and ham-fisted accurately describes the writing in all of Bethesda's games. I hope they hire real writers for their next game.
one day someone will make a mod that re-writes the entire storyline for fallout 3 into something awesome.
unless they already did.