Godwin's Law only applies when the anology is ill-fitted and done in the heat of the moment... which is not the case with either the Thalmor or the Enclave. They're both pretty clear cut anologs.
The only anologs is their distaste of other species. That's it. Nazism is so much more than just blindfolded racism. It's a political ideology, a way of life, an economic model and was close to becoming a religion. Let's see why the Enclave does not compare with Nazism:
- The Enclave is democratic by principle, while Nazis detested the very idea.
- The Enclave has full gender and racial equality among humans, something that the Nazis once again opposed to the core.
- The Enclave allows women to serve side-by-side with men in armed forces. Nazis did not allow this, even in their last moments.
- The Enclave takes pride in America, while the Nazis viewed America as the root of all evil.
- The Enclave is carries on American capitalist values. Nazi Germany employed an economic system of Corporatism, which meant domination of large, state-supervised corporations with little room for personal initiative.
- The Enclave considers itself the only humans on earth and classify mutants as other species, while the Nazis targeted individuals they considered human but still sub-human.
And much more.
Most of the above apply for the Thalmor as well, though there is little we know of the faction.
EDIT: The reason I'm dragging elements of other games here is simply that I resent Nazi comparisons where they do not apply.