I've actually been really torn on the issue of what side to choose, without spoiling the plot of the actual quests themselves, why should i choose the stormcloaks? for each of your reasons I have a counter reason (and i am not partial to either side):
- the empire may be in worse times, but what do you expect? after the oblivion crisis they had nothing, had to appoint someone, and the thalmor used that to slowly take over
- in the end of the great war the only way they were able to fight off the thalmor was via the hammerfell rebels joining with the empire, how can they possibly hope to fight off the thalmor if every state becomes independent, potentially warring with themselves, just waiting for the thalmor to come and pick them off one by one?
- do we really think that completely independent states would be a good thing? what about for the other races? ulfric is racist as FUCK and many people are, you can see it in the dark elf persecution. racism has been a pervasive theme throughout the elder scrolls games since morrowind, how are the other races going to do if ulfric and his racist armada takes over? some sort of genocide would not surprise me at all
- do we really need nord supremacy? my character is a nord, but i get the vibe of nord supremacy throughout all the stormcloak areas, and honestly i don't see why that is better than the empire
- the empire didn't just surrender worship to talos for kicks, the war was insanely bloody and awful and if they didn't give in they would've been crushed; they fought and eventually gave up so it wasn't like they just from the start said OH FUCK YEAH FINALLY WE CAN OUTLAW TALOS, it was forced upon them. the empire didn't want to secretly outlaw talos worship
- the empire when it comes down to it, just like the stormcloaks is a group of people. there may be fucked up areas, fucked up forts, fucked up leaders etc, but in the end they're just trying to keep the peace and restore the kingdom. they may not be as good as the septim dynasty (though they also were insanely brutal and harsh) but i don't see how state rule would be any better.
if people can give me some hard evidence as to why the empire sucks, why the empire will continue to suck, and why state rule would be better than i will gladly join the stormcloaks. as of right now i think both of them have their positives and both of them have their negatives, but i'm slightly leaning towards the empire because the only way to fight off the thalmor would be a united tamriel (they've used the fragmented empire to gain power before such as in elswyr) and the potential genocide that could erupt from ulfrics racist regime would be devastating for everyone but the nords in skyrim, potentially following in other provinces.