[Spoiler Warning: Spoilers for Fallout 3, DLC Broken Steel & Fallout 4 (minor about who is the BOS elder in Fallout 4)]
The ending of Fallout 3 performs a solid job of painting the Brotherhood of Steel as the good guys and the Enclave as the bad guys. Using overblown historical examples, the Brotherhood of Steel are portrayed as knights of virtue, peace and good will; whilst the Enclave is portrayed as jackboot Nazi’s who want to sterilise the Capital Wasteland of all undesirables.
This portrayal is important as it affects your judgment of both factions in Fallout 3.
In Fallout 3 (and all Fallout games actually) you have no choice in whether you side with the Enclave, aside from using the modified FEV virus (which we will get to in a sec). The Enclave are locked in as the bad guys and Brotherhood of Steel as the good guys. Fallout 3 conditions you throughout the story to make you feel like you are making a morally righteous "decision"; that of destroying Raven Rock, murdering countless soldiers (who have families - we know this from Fallout New Vegas) & turning Colonel Autumn into a pool of Plasma.
It's a fact that bad guy = pool of plasma...
The Enclave may be classically definable as evil, but when it comes to politics and power there is rarely such an apparent contrast available (except maybe Nazis or Hillary Clinton/Donald Trump).
Dated political jokes aside, when it comes to the safety and security of the capital wasteland, we really think about which of these organisations will have the greatest positive impact on the region; without appealing to higher virtues like truth, honesty, freedom, etc.
Basically, which of these organisations is the best one through a Real Politiks lense?
Project Purity - Why the Enclave are the good guys
Fallout 3's main storyline centres around Project Purity and the battle for who controls it. So this project should be a key factor in your decision-making process as to who should be in charge of the capital wasteland. There can be other factors that could influence your decision but we are going to just focus on project purity.
The battle for the wasteland is like every US Presidential election in modern history, it’s a two horse race (yes there are third parties, but come on we all know its really going to just be two candidates). Like a voter you must choose between one candidate or the other (unless you abstain, which in video logic is basically putting down the controller and refusing to play).
So let’s look at these candidates.
First, you have the Enclave, who are the continuation of the US government after the great war. They are racial purists, who believe that after years of isolation, that only Enclave members and sealed vault dwellers are true humans; with all the other humans corrupted by radiation. They are a heavily authoritarian regime, and whilst they claim to have a president; all evidence suggests it is a military dictator. So in one corner, you basically have Nazis (kind of) and in the other corner, you have the Brotherhood of Steel, paragons of justice, who help the community and care about the capital wasteland.
So this should be easy right? How can anyone choose the evil Enclave over the kind & virtuous Brotherhood of Steel?...Here are a few reasons.
Stability and Unity - Why the Enclave are the good guys
As fans of the games are aware, the Brotherhood of Steel aren't normally kind, caring & altruistic; they are actually bigoted, xenophobic, hermit-assholes. The Brotherhood of Steel don’t normally care about people, they are a quasi-religious fraternal order who’s primary mission is to seek out and confiscate technology that it deems too dangerous to be in the hands of the common man.
This primary mission was one of the three goals that Fallout 3’s Elder Owyn Lyons was tasked with achieving, before being sent to the capital wasteland by the Brotherhood of Steel Council. The other two goals were: 2. To reconnect with a Brotherhood of Steel chapter that the council lost contact with and 3. Discover the source of the super mutants in the Capital Wasteland. Upon arrival in the Capital Wasteland, these goals changed; with the main goals that guide the Brotherhood of Steel being pushed aside for more humanitarian goals. To preserve order, the humanitarian goal wore the thin veil of finding the source of the Super Mutants.
Project Purity became an important strategic asset for the Brotherhood of Steel, as it would produce clean water which would help the people of the Capital Wasteland and it would also prevent further genetic modification of humans. Whilst Project Purity isn't exactly 'finding the source', its is complimentary to this goal and helps prevent the creation of ghouls (and maybe mutants, whose origin were initially unclear until the end of the game). This thinly veiled goal is enough to satisfy most Brotherhood of Steel Members, with only ultra-orthodox members openly declaring that ‘Elder Lyons has betrayed the order’.
Now, let's skip ahead 10 years for a second and have a look at Fallout 4.
We learn that Arthur Maxson has become the Elder of the East Coast Brotherhood (and then high elder) and his reign is very traditionalist. This is a very quick turn around in the Brotherhood of Steel, changing from a humanitarian organisation back to the traditional, military order it is in Fallout 4. This means that in the 10-year gap between Fallout 3 and Fallout 4, the Brotherhood of Steel very likely divided into traditionalist (Maxson) factions & humanitarian (Lyons) factions; with the traditionalist faction winning in the end. This factionalisation would be incredibly hazardous to the organisation, as resources & direction would constantly be shifting (think of it as a minority government, lot of infighting and not doing a whole lot of work getting done).
Contrast this division with the Enclave's stability...
Whilst President Eden in Fallout 3 is stated to be ‘in charge’, it is very clear to the player that the one really pulling the strings is Colonel Augustus Autumn. Colonel Autumn appears to be in his late 40s – early 50s, and the East Coast Enclave's mission conforms with the organisation's core goals; that of restoring the former US government. So it is safe to say that if the Enclave took over the capital wasteland, that they would have a stable government headed by Colonel Autumn, and that his reign could last for 20 - 30 years.
The longevity of a stable Enclave government would provide stability & clear a direction forward for the anarchy of the Capital Wasteland.
Water delivery to the masses –Why the Enclave are the good guys
The next thing to consider is that the Brotherhood of Steel unintentionally created a black market and a war on drugs, the latter of which they lacked the will & desire to fight it. The drug I am referring to is purified water.
How is purified water like a drug?
Easy! It is a restricted chemical that people feel they need in order to carry on with their daily life and will pay a high amount of money to obtain. Now as many anti-war on drug advocates will argue, wars on drugs are expensive and ineffective; arguing that solution is to 'just legalising it man’.
An important thing to note is that the Brotherhood of Steel directly state that they do not want raiders to get the free water, whilst The Enclave have never said it but their goals of unification and reestablishing a government, leads me to think that they would also avoid giving it to Raiders. As the Raiders can not have access to purified water, it increases its scarcity. Commodities that are scarce and in high demand, have a very high financial value.
So both the Brotherhood of Steel & the Enclave would have made the purified water transports way more valuable to raid; because if a Raider can get a large quantity of purified water; they can sell it for the same price as bottled purified water to other raiders and make a huge profit.
Basically, it's like you getting water from your tap selling it to someone for $5.00 (times 1000).
To combat these increased raids (by Raiders, whose job description implies they do this a lot) you would need a security force that is committed to ensuring the outcome of the project and concern for the people the project serves.
The Brotherhood of Steel are not the best people for this job, as I outlined above, their goals are not ‘protect the people of the wasteland’. Consider that once Project Purity is in action and the cause of the Super Mutants on the East Coasts is resolved (which happens and is part of the reason why Arthur Maxson become the Elder in Fallout 4), there is very little holding Brotherhood of Steel members to the goal of protecting water shipments. Contrast this with the Enclave whose goal is to set up a stable government.
The Enclave are entirely focused on serving the community; not for moral reasons but for pragmatic and ideological ones.
They would likely to send more patrols on water caravans, murder all of the slavers in Paradise Falls and slowly wipe-out the Super Mutant menace. They would probably be incredibly brutal to Raiders, as they would want to send a message to the people of Capital Wasteland that the Enclave is the ones in charge now. There is so much going for the Enclave in ensuring safe water trade routes that they would commit more resources and stay focused on the project longer. In fact, Colonel Autumn even says this about the Enclave and their commitment to the Capital Wasteland.
"Once you're dead, we'll finish off this pathetic Brotherhood and become the true saviours of the Wasteland"
- Colonel Autumn
So if you are with me this far, I hope I’ve convinced you that the Brotherhood of Steel is not an organisation that should be in charge. The Enclave want to establish the government and the are way more committed to enforcing Project Purity than the Brotherhood of Steel.
'You forgot something..." Did I? - Why the Enclave are the good guys
Now, I know what you are thinking now, you have your trump card and it’s one that will blow my theory out of the water entirely. You’re thinking about the modified FEV Virus and how devastating that would be on the Capital Wasteland.
If you are thinking that, then you are absolutely correct in that it would be completely devastating. If the Enclave had enacted that plan, there is no way to defend their actions. It would be like defending Nazi’s after the Holocaust; you can try doing it but you're wrong.
However, in Fallout 3, it is the super-computer President Eden who asks you to add the modified FEV Virus to the water source. After you meet him, Colonel Autumn assumes control over the Enclave; in a coup prior to his death. When you confront Colonel Autumn about the modified FEV virus, he tells you that this plan was rejected by him months ago.
So if where Colonel Autumn became head of the Enclave (as he does briefly at the end of the game), there is no way the modified FEV virus would be added to the water; unless you did it behind his back (in which case it’s not really the Enclave who are evil...it's you).
So under Colonel Autumn, there would be no mutant genocide and only an authoritarian organisation committed to rebuilding the US government and helping the people of the wasteland. Not great, but in a world where you have the choice between an ineffectual government body or a dystopian anarchist hellscape...most people would choose authoritarian stability in a heart beat.
In the end, even though the story of Fallout 3 paints them as bad guys; they are technically the best choice for the capital wasteland, and should be considered the game's good guys.