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.
Okay, I get that the Stormcloaks are a bit sus, and clearly nationalistic but they're not Nazis. I'm just saying, the only side that has random citizens get sent to camps and prisons are the Empire.
They even let you join if you're a non-Nord so long as you respect their customs. And Ulfric himself is smart enough to not spark a race war in his city despite a huge population of Dunmer and Argonians.
Not to say they're good but more that they're just sort of a weird ideology and can't be reduced to "they're Nazis".
The actual Nazis though, the Thalmor, are given free reign to harass, torture and murder innocent civilians by the Empire. The Empire wags their finger but ultimately cave to their every whim. Several religious individuals go missing after an Imperial victory and are not seen again.
Despite their victories over the Thalmor they decided the war was too costly to their core regions and caved to grossly imbalanced demands. Hammerfell didn't cave and managed to win against them despite the whole-ass empire claiming they can't. Weird that.
Going past that the Empire are also horrid racists themselves. The moment they're given access to the holy Island of Vvardenfell they immediately plunder its resources and attempt to convert the locals to their own religion. Then, despite their membership in the Empire, the people of Morrowind are given no aid when the Oblivion crisis occurs and are left to defend for themselves. The Empire actively pulls legions out of Morrowind back into Cyrodiil during this crisis. Then the Red Year occurs and the Empire gifts Solstheim to the Dunmer... Oh wait no. That was actually the King of Skyrim. Weird that.
The Stormcloak holds of Riften and Windhelm even have accepted and integrated refugees from Morrowind as well.
tl:;dr Despite their reputation, the Stormcloak are not only less horrid than the Empire, but are honestly less xenophobic than most other of the provinces, despite some of their shortcomings.