Why does the "Good Faction" of Fallout 76 involve aligning with villains?
Something that I found rather peculiar about the "good faction" in Wastelanders is that aligning with them involves working with one person who engaged in some vicious anti-worker practices (in the name of profit) and a group of people that the original Fallout explicitly informs the player had engaged in some horrific actions in the name of American imperialism.
(ง'̀-'́)ง SPOILERS (ง'̀-'́)ง
With the expansion of Wastelanders, Fallout 76 presents two main factions - the Diehard Raiders of The Crater, and the settlers of Foundation. During the course of helping Foundation, you encounter Penelope (Penny) Hornwright, who was a senior executive at her father's company, Hornwright Industrial. You can find out (before meeting her) that she hired strikebreakers to deal with protesting miners, mandated 24 hour shifts for Hornwright employees, and modified the air purifiers for the Clear Skies Alliance that lead to them becoming ash forges, polluting a significant portion of Appalachia (we have the region known as the Ash Heap now thanks to her actions). Can you speak with her or confront her about any of these horrific actions? No.
Then there are the remnants of the U.S. military, and let's keep in mind that one of the first scenes in the original Fallout involved the military murdering civilians before live television and then waving to the camera. The remnants of the United States Army, led by Captain Oliver Fields, seems intent on the restoration of the Old World that lead to the apocalypse. If you try to explain to him that "America's over" his response is: "Don't you know a lick of history from before the war? We've always been forged in fire. Maybe we got a bit burnt this time, but I can't believe it's the end."
Jen is good. Comparatively she lacks the moral issues that come with Penny, one of the wealthy elite who committed a lot of horrific actions in the name of profit, or with Captain Fields and his remnants of a military who may likely be culpable of war crimes given what America was doing before the Great War.
I'd say the biggest issue is simply one of missed opportunities given that she could have been a window into another perspective that we, unfortunately, don't get to explore much, as both a Chinese-American born in the wasteland of a country that targeted and persecuted Asian-Americans, and as the daughter of parents who were from China.
Conversely, the villainous faction of the Diehards at The Crater, led by Meg Groberg (voiced by Mara Junot, who also voiced the fantastic Nyoka, legally Nyoka Ramnarim-Wentworth III, of The Outer Worlds), is fairly different in terms of the people who we interact and work with for the main mission.
Working with the raiders involves working with a mute raider, Weasel, who uses a modified collar to communicate (which is limited in the capacity with which she can express herself, which at times frustrates her due to the limitations).
A suicidal ghoul, Lou (who is worried he might hurt people if he goes feral because being a ghoul is still new territory for the denizens of the wasteland). You can even help him deal with his feelings about being a ghoul once the heist is over.
A child raider, Ra-Ra, who has no idea what America even is.
And Ra-Ra's surrogate parent, the Super Mutant named Gail.
After you align with Meg and the Diehards instead of Foundation, you're tasked with wiping out a group of raiders who defected from Meg's leadership because they are bigots.
In short, the "evil" main faction involves wiping out a group of bigots before pulling off the heist.
Meg makes it abundantly clear that intolerance towards people who are different isn't acceptable.
Then Steel Dawn adds a group known as the War Party among the Diehards of The Crater, and one of the raiders among their number, Burke, is nonbinary.
The contrast between the two main factions does make me question some things (particularly the morality of working with arguably evil people in the name of the Greater Good) since the people you recruit for the settlers of Foundation feel like working alongside the Fallout equivalent of Reed Tobson and Spacer's Choice while the Diehards of The Crater you work with during the narrative feel much more interesting in comparison.