Does anyone agree that neither the Empire nor the Stormcloaks are really the villains? I'm playing the game and I can't help thinking that they're soo blind to the fact that they're both being manupulated by the real Nazis of the story, the Thalmor! As I see it the Thalmor are just using both sides behind the scenes to get eventual power for themselves, by getting their enemies to destroy each other whilst they simply sit back and watch from the sidelines. If so, can anyone see a future military confrontation with these characters, just as we had to do in real life WWII with the Axis?

I agree. Thalmor are the real villains. The Empire however has grown weak over the decades, and thus had to submit to them. However, I'm still with the Imperials till the bitter end. I don't agree with whatever the Stormcloaks think they're doing.

I get the impression, either way the thalmor win. Knowing humans... the Thalmor just have to wait 50-60 years, pulling their strings, whispering a word or two here and there , a knife in the dark here, a lil bit of poison there... because in 50 years or so , folk will have forgotten why they were fighting in the first place.

The Thalmor are glad of the Civil War, it's weakening the Empire AND Stormcloaks while they sit and watch from the sidelines.

If you take your time to talk to both Stormcloak and Imperial supporters, I think it becomes pretty obvious that their conflict is definitely not a villain-hero situation. A lot of NPCs are also not bling and are aware that the side they support is not crystal-clear and they sort of pick the "lesser evil". For example, try asking Jarl Laila the Law-Giver what she thinks about Ulfrik. The PC picking a side is just that - picking a side, not choosing the good guys.

And the Thalmor being villains imo is made pretty clear during the game - both with what happens and what is said. The fact that Thalmor convoys are not aggressive towards you on sight does not matter here.