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.