"...with great power there must also come -- great responsibility!" - Stan Lee, 1972
Fallout is...complicated in it's scope. Yet we are teased with every entry with a familiar dialogue to set the tone. It establishes the theme that although humanity may progress through technological marvels or may improve with a change of flag...we are still left with the uncomfortable reality that humanity is inexorably tied to war. Whether it's tribes, towns, factions & or nations, there is always a conflict stemming from ideas on how humanity should govern itself following the disaster of a mass nuclear arms exchange.
Between former military veterans that struck a chord when they got to meet Boone and developed a fondness for the NCR, to those who have found a voice in Caesar's Legion (and yes, those people arguing for that type of fascism do in fact exist unironically, it's not just a meme); There's a group that represents a distinct set of values that each player can resonate with. Better yet, discussions with faction representatives (Paladin Hardin, Vulpes Inculta, Veronica, Boone, etc.) all yield a varied viewpoint that offers a perspective to better flesh out and humanize some of the perceive-ably dirty actions of each group.
However, despite this varied approach that allows for user input and world reactivity to said choices, there are still those who seem not to grasp the importance of this approach. Whether it's those who would make arguments on who is the best for the wasteland or Bethesda's attempt at factions in Fallout 4 feeling more Black and White with little input on the players part. They are both flawed perspectives that fail to grasp the message of pragmatism that the games set out with from it's debut to the last hurrah of some of those original developers during New Vegas.
There is no right solution. Whether it's the NCR's bureaucratic nature & imperialist Manifest Destiny 2.0 reaching East instead of West, Caesar's disregard for equal opportunities among the sexes, House's benevolent dictatorship, or the instability raised from creating a power vacuum when using Yes Man as your key to the Strip's Gate. Each decision yields distinctly negative features, but we treat those inconveniences as having been worth it. The ends justify the means, as the player is the one to flip the switch on the electric chair for a numerous number of competing fringe factions.
However, with Fallout 4 the good and bad guys become much clearer. Arguments could be made over the false mask setting a stereotype that paints the Railroad in a negative fashion for keeping secret those who could be 'mentally ill' or prone to glitch to be more apt; But in all honesty you end up looking like an asshole for siding against the group who is modeled after an Anti-Slavery group. The same can EASILY be said about the Minutemen whose sole purpose is protecting people from Raiders through mutual defense arrangements. This approach, while it creates some wonderful characters, falls flat in the face when compared to other titles within the same franchise.
Am I saying that there are no redeeming values to creating black and white characters? Not at all. New Vegas had plenty of irredeemables & folks with good intentions. The difference being was that leadership is always questionable. McNamara (named after Robert McNamara, a very controversial figure for Project 100,000 during Vietnam) is playing it safe to a fault, Hardin is clearly an extreme zealot in the flavour of the original BoS of Fallout 1 & 2, and General Oliver has screwed over Hsu, a far more level headed option for being the intermediary for acquiring new territory on their frontier.
All in all, Fallout is NOT about who is right. It's about what choices you can sleep comfortably with having made and how the decisions of others have massive ramifications on the world around us. This is confirmed by Tim Cain's Post Mortem Keynote at the Game Developer's Conference in 2012 through his mention of players need to immediately replay the game to deal with the questline regarding Killian & Gizmo. You are not playing Civilization, you're playing an Empathy Litnus Test with Action RPG mechanics.
I've heard some folks complain about the role of The Courier. How even with that loose of a designation it feels like the role is too big for the Mojave. I have to disagree. You are meant to be someone of an exceptional nature. Someone who could mirror our world's own cultural heroes or villains by the way they influence those within their affect. By the nature of design, you can learn how actions have consequences for a large number of people.
I hope you've found this informative even if a bit redundant. I appreciate you reading this morning mind vomit. Peace & Goodwill.