Sort of different from your typical stormcloak vs. imperial thread. What are some of the similarities between both groups? Here are two points I came up with.

* One thing is that after the civil war they both plan to drive the Thalmor out of skyrim (though it never happens in game for either side).

* The Dragonborn makes a difference to which ever side is the "winning" side.

Is there anything else?

You forgot that The Dragonborn makes a difference to which ever side is the "losing" side.

They both have considerable support from the local populations.
They both are motivated by legitimacy, rather than economic or even strategic aspects.

There's also the fact there two leaders think very similarly and would be friends if the situation was different.

In the words of Eorlund Grey-Mane:

"At the end of the day, Stormcloaks and Imperials aren't that much different. Both wants to tell you how to live your life."

Eorlund said that?!
My respect for him has just grown, I thought he was a mindless stormcloak like Vignar...

Yes, he does say that if the Stormcloaks takes the city and you ask him about it. He doesn't seem to care much, though he appears slightly more in favor of the 'Cloaks when we include the rest of the quote.

"At the end of the day, Stormcloaks and Imperials aren't that much different. Both wants to tell you how to live your life. But I guess I rather hear it from a real Nord than some Emepror down south."

One thing i see in common is this, Stormcloaks are Nords and the Legion also includes Nords, so Civil War not just between Ulfric and his Nords and the Empire but also Civl War against other Nords. So he makes war on other Nords, i think that says it all about him. Power hungry criminal.

The same was true of George Washington. His army fought not only British Regulars, but Loyalist Militias made up of American's fighting for Great Britain. I guess that is why we always see Washington hailed as a power mad war criminal as well.

*Cough* He was a power mad criminal *Cough*