The funny thing is that Elder Lyons isn't actually all that nice of a guy. People prefer the Midwestern Brotherhood of Steel because they're "hard men, making hard decisions" while Elder Lyons tries to be all saintly but he's actually a bit of a fanatic. The Enclave talks a good game about genocide but they've never actually done anything impressive other than the massacre of one vault of intelligent Death Claws.

Elder Lyons, on the other hand, decided out of hand to annihilate an entire Wasteland civilization with the "Scouring of the Pitt." Yeah, people talk about it being a real **** hole but so was Vegas Pre-House and people point to that as a big sign of House being a guy with serious ethical issues. The Great Khans are, uniformly, the Post-Apocalypse version of a Meth-Dealing Biker gang. However, almost everyone agrees Bitter Springs was a horrific massacre.

Elder Lyons, by contrast, points to the Scouring of the Pitt and goes, "Yeah, I am AWESOME for that."

Yeah, Elder Lyons has abandoned the mission of acquiring new technology for waging war on Super Mutants but it's pretty easy to also note that he intends to stay in the Capital Wasteland and build his own little empire. Rivet City talks about how it's not comfortable with the Brotherhood of Steel having control over all of the water but effectively he and his men are now the de-facto government.

All for everyone's good, of course. I'm not saying Lyons is actually a devious Machiavellian manipulator. The irony is that he's doing all these things for people's own good and pretty much ignoring any possible moral objection. This, of course, all the while as he's taking pot-shots at ghouls amongst other mutants.

Given they didn't take any mutated children from the Pitt, the guy is a giant racist too. Just like the Enclave. Not to mention a kidnapper.

It's interesting to apply the moral ambiguity of NV to the original F3 games. Just because people THINK they're heroes, doesn't mean they actually are. Let's face it, the entire ending of Fallout 3 isn't remotely related to whether or not the Capital Wasteland recovers or not. The Enclave or the Brotherhood of Steel is going to do the exact same thing either way. Both will set themselves up as the de-facto governments of the Capital Wasteland in exchange for water.

The only difference is the Lone Wanderer gets to avenge his father if he sides with the BOS.

Edit:

This actually lead me to write an essay on the subject for my blog. http://unitedfederationofcharles.blogspot.com/2012/08/the-morality-ambiguity-of-brotherhood.html

http://www.stephenburch.com/noise/grey_scale.jpg

He is one or two left of white.

Also hating a ghoul doesn't make you racist, it makes you a "bigot"...unless the ghouls is black.

I dunno.

Let's face it, at the end of the game you've:

* Re-introduced Feudalism into the Wasteland.

* Handed the keys to the kingdom to just another faction feuding for control over a Maguffin, not prevented it from being turned on.

* Gleefully ignored the fact Lyons lead the cleansing of all mutants in the Pitt and kidnapped their kids.

* Have supported him despite the fact he's proven unable to keep his merry band of knights together and win a war against the Super Mutants.

* Given the Water Purifier over to a faction almost identical to the Enclave (at least under Colonel Autumn).

* Given the Wasteland over to the man who is responsible for Ashur (who represents the Dark Side of Lyon's ideology made manifest)

At the end of the day, Mister House's criticism of the Brotherhood is most apt with Elder Lyons. They're a group of people playing at being Knights of Yore.

The only reason they survive is because of their own personal Galahad/Lancelot who comes to save them at the last minute.

In 200 years, the CW may prosper but it's not going to be a Republic like NCR. It's going to be a monarchy because that's how the Brotherhood works.