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.
Honestly the incompetence of the NCR started to piss me off. It seemed less like a natural criticism of their politics and more just like they were being written as dumb.
Like, I'm sorry. They can apparently afford to send a hitsquad after you but can't break through a barely fortified squatting "camp" like Nelson. To the point where morale dropped heavily but only on the NCR side for some reason.
Legion excel at guerilla warfare. It's why they lose Hoover Dam, because NCR had an actual plan and why it takes like 4 years to even try again.