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 whole central theme of FNV is that humanity needs to let go of the past and chart a new path for the future. NCR, House, and Caesar are all attempting to recreate some idealized past vision of civilization, and as a result are all critically flawed and doomed to repeat the same mistakes that ended civilization the first time around. Independent Vegas is the only good ending.