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 games are products of a liberal world so naturally their "good guys" are just less worse than the bad guys. Hardly anybody worth cheering for in any of the "good" factions in those games. People think its due to good writing - grey characters, moral ambiguity, forcing harsh choices, but the choices are all quite narrow in the end because of the horse blinders of liberal ideology.