Except a big difference between the stormcloaks and the Thalmor is that the stormcloaks want any non-Nords out of Skyrim. If the Thalmor only wanted non-Altmer or non-elves in the Aldmeri Dominion, they could just close their borders, put up some big "all humans stay out" signs and go about their business.
However, they are in another province, actively trying to force the Nords to stop worshipping Talos. If they only wanted to keep humans out of elven lands, why would they be doing that? Doesn't make much sense to want other races out of your empire, but then insist on sending your own people into humans lands. The forcing of stopping Talos worship is a big step in their plan to un-make the world, so you can't really say they are like "elven stormcloaks" because they have completely different goals.
Not saying the Nords haven't been really bloodthirsty and brutal towards elves, because they have, but that's not really the point. The Stormcloaks and Thalmor just aren't comparable political-wise.
True, of course. It's pretty hard comparing things with so many variables without simplifying them or focusing on a few aspects. But if we go back in time, most provinces belonged to Mer. High Rock was elven, Hammerfell was Elven, Skyrim was Elven. Skyrim, and later other provinces, were wrested from the Elves through bloodshed. Same with Hammerfell, which was conquered by the Redguards, just that this time it wasnt just Atmoran invaders vs Elves. And its true that it was quite some time ago, but for a race which can live for centuries rather than decades it may not seem as distant.
And also, why they persecute Talos worshippers is pretty understandable, theological reasons aside. The Empire promised to stop the worship of Talos in the WGC, and going against it would be breaking the peace treaty. To make a comparison, had Redoran lost a war against the Nords and promised to pay them 100 000 septims as an annual tribute and they ended up saying "Nah, don't really feel like paying you a single coin after all." then some kind of reaction would be expected. Both in retaliation and for the enforcers of the treaty to save face.