Keep in mind: I'm basing the following on them being the best available options that the games give you, not that they're objectively the best conceivable choices ever.
For Skyrim: Fuck the Stormcloaks. They're basically medieval Nazis.
For New Vegas: Fuck Caesar's Legion. They're basically Neo-Roman Nazis.
But even with the independent New Vegas routes, whether it be with Mr. House or you at the helm, I feel like the NCR is still overall better. They're by far the most organized, have the most resources at their disposal and are arguably the best hope for humanity's collective survival/recovery post-apocalypse.
Counterpoint: The NCR may be better organized, but it's also riddled with the same corruption and imperialism that led to the Great War in the first place. You go with them and they smother the people with taxes and heavy-handed policing
Mr. House is a Autocratic Techno-Fascist, the people thrive, but are yoked to an automated police force that will just as gladly ventilate you for littering as for trying to rob a casino
The Legion are fascist slavers, it shouldn't be hard to grasp why they're terrible.
An independent Vegas, operating with a unified populace is definitely the best outcome. The Kings, the Followers, the Brotherhood, the Khans, the Boomers and the Casinos can be made to see working together is the best path. They might not be as organized, but with the Securitrons providing security from outside threats, it's the option that allows the most self-determination and control over the means of production.
Can you tell I've put like 800 hours into New Vegas?
Also, an independent Vegas with the courier at the helm has the advantage of hi-tech R&D from the Think Tank and an incredible abundance of resources from the Sierra Madre vending machines. If the courier plays it right they could create a post-scarcity world out of a post-nuclear one.
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