Besides the fact that the protagonist isn't wearing Stormcloak armor and might not be even be a Nord, which makes him (or her) stand out from every single other Stormcloak who was captured? It's made clear in the opening that the Empire knows the protagonist isn't with Ulfric, and they still plan on killing him (or her).
It is made clear that ONE person don't believe so. That is irrelevant: If I sit in a buss with a terrorist, I don't think they would look at my clothes.
The point is: the people in charge don't care.
Welcome to the world?
Nobody cares, that is a fact. They had Ulfric, they had the guy who started the war. If people feel sore about that, I suggest you head to the army for a year. You mean nothing unless you've earnt it.
You mean letting an innocent person go because he or she clearly isn't a member of the rebel cause, or executing them?
Or perhaps letting go a general of the Stormcloak, which didn't wear the Stormcloak clothes in said moment? One life means very little in a war. There is nothing "clearly" about it, Hadvar said what he said out of a gut feeling. No facts were there, and it would take long to prove anything. They didn't want to carry you all around for no reason, when you are in a VERY bad position.
Your claim that you weren't trying to make this black and white would work better if you weren't trying to cast the Stormcloaks as WII Germany.
I claim I don't see it in black and white, I also claim I prefer the Empire over the Stormcloak. I have also had opinions on both side: I see the war as a grayzone, I see tullius vs Ulfric as black and white. I would shoot Ulfric on sight if I was Tullius.
If that was the case, Ulfric would have kicked out the Dunmer from Windhelm. He doesn't. Ulfric is even willing to name a Dunmer as his Thane and give him permission to purchase a mansion. Also, Ulfric spares the Jarls who opposed him, he doesn't simply kill everyone who gets in his way. As for the Empire: torture chambers and letting the Thalmor have free reign in Skyrim doesn't sound much better. Some of the Legion even contemplate trying to re-take Morrowind.
Have you seen how the Dunmer live in Windhelm? They might aswell be thrown out. They are under no protection what so ever.
Ullfric challenges Jarls, and slaughter people. A certain book, which I forgot the name of, states that he slaughtered anybody that did not help him fight the Fornsworn. So any man that could carry a sword, but denied to fight, would die. That is slaughter and murder, and shows how he acts: Power hungry and selfish.
What "good long term goal"? Hammerfell was able to take on the Dominion without any aid from the Empire, and keep their autonomy. I don't see why Skryim couldn't do the same.
Last time Hammerfell won against the Thalmor, they had some disguised Imperials with them. They are also known to be pretty good fighter, and havn't had both a civil war and dragons on their head for the last years. Skyrim is weak as of now, and the Thalmor is ready to invade any second.
The Empire would be ready to attack the Thalmor. Guess which idiot stopped them? His name starts with U and he started a rebellion.
Tullis and Ulfric hate the Thalmor, but the Empire is going to appease them while Ulfric is going to kick them out of Skyrim.
The Empire appease them because they need to. They are weak, and need to rebuild.
You mean kick out the small teams in Skyrim? Sure, go do that. Wait for the army a month later, and see what happens. It would take Skyrim a few years to get the army needed to hold itself against the Thalmor, and pushing out the Thalmor from Skyrim would not help anybody.
At least the Empire knows strategy: fighting when you are strong, not when you are weak.
Restore Talos worship, maintain their autonomy, and kick out the Thalmor. Sounds like they have a plan to me. I'd say there are different benefits when it comes to siding with either the Legion or the Stormcloaks, but I think Ulfric is a more capable leader than Elsif, who will evidently be little more than a puppet leader for the Empire if she took the throne and became High Queen.
As said earlier: Do that, and you got an invasion. Cyordiil almost fell to the invasion. Hammerfell did as well. Skyrim had had civil war for a while, is in chaos, had dragons -- they would be no match. Good plan, huh? Kick out 20 Thalmor, get 5000 back. There is a reason they banned Talos worshipping: It prolonged the time for an invasion. Just "enough" time for the empire to rebuild, if it wasn't for Ulfrics rebellion.
You mean people without magic fighting people with magic, like in Hammerfell, the nation that fought and maintained their sovereignty from the Dominion even after the Empire sold them out? The Thalmor didn't win, forcing the Aldmeri forces to withdraw completely from Hammerfell.
Seen the college? There are what, 5 people?
Nords hate magic. There are max 40 mages in all of Skyrim, when every Thalmor is a mage/battlemage. Who do you think win:
1) The team with a strategy, wear light armor - but sturdy, can use healing magic and is very skilled with a sword
or
2) A team with no strategy, wear fur and usually wears a 2 handed weapon.
Ulfric challenged the High King to a duel following Nord tradition, which was accepted by Torygg, and High King Torygg lost
Do you know what a duel is? It means a fight between 2 people testing skills.
Ulfric knew Torygg couldn't say no, and he also knew he was stronger. Now that is the first thing that was wrong.
Secondly he used a shout. Which is against the term "duel".
Thirdly he killed him before he could get up.
Basically: I set you to a nuke, and shoot you with a rocket launcher, and a bath of acid falls on you, and you only got a dagger to fight me. That is how honorable and fair that fight was. Not a duel: Murder. If Torygg knew a shout, then it would be a duel -- but he did not.