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.
The Legion is so outrageously hypocritical (enslaving women and rejecting all technology and except that which benefits them militarily or their leaders personally) and obviously a dead end for humanity that I could never bring myself to even attempt their path. As interesting as Caesar is as a character the Legion path is basically the "Stupid Evil" path. You have to be a serious sucker to think they would have any ending other than disintegration after Caesar's death.
That was usually my main issue, they were just absolutely heinously shitty to the point that they just seemed like raging goobers. There was no way that I could effectively role-play wanting that shit, and I deliberately played a stupid and misanthropic character with like, 2 or 3 intelligence and he still seemed like he would be too thoughtful not to just have contempt for their whole project.
The funniest thing is watching fascists worship the Legion, while completely ignoring the fact their legion, as Ulysses puts it, will simply collapse back into anarchy the day they reach the pacific. And even if they survive the NCR, what the fuck are they gonna do ? Make a "slavocracy" ? Worked out pretty well in history lmao.
There's zero chance the Legion could win a prolonged war against the NCR. The NCR has an exponentially better logistical situation than the Legion.
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.