Imperials vs Stormcloaks: Imperials for Tamriel, Stormcloaks for Skyrim
Saadia vs Kematu: Kematu
Corrupt or purify the star of Azura: Purify
Which of the three (four?) captives should be killed: the cat and woman
Dawnguard vs Vampire Lord: Dawnguard
Faendal vs Sven: Faendal
Cure lycanthropy: cure
Spare or kill Cicero: spare
Spare or kill Paarthunax: spare
Spare or kill Madanach: kill
Spare or kill Barbas: spare
Spare or kill Sinding: spare
Spare or kill Motierre: spare
Imperials vs Stormcloaks

Let me get the obvious out of the way: the objective is to fight the Thalmor, not to quell the rebellion or destroy the Empire. The elves might be smart, good at magic, and have some nice armor, but their government (and maybe they too) are some awful cunts.
If Ulfric wins, Skyrim is independent, and the empire is confined to High Rock and Cyrodiil. Were the Thalmor to invade the Empire, they would surely lose without allies — Skyrim wouldn’t help, neither would Hammerfell. In the event of winning the Civil War, Ulfric seems to be set on fighting both the Thalmor and the Empire, which is quite short-sighted, though the Thalmor don’t pose that much of a threat to Skyrim in the short term due to territory.
If the Empire regains control, it’s likely that focus will fall back to the thalmor; Tullius himself hints at it after winning the war, and everybody seems to be expecting a second war. Nobody but their supporters like them, regardless of whether their alleigance lies in the war. With High Rock, Skyrim, and Cyrodiil (perhaps even Hammerfell?) united, the Empire has a good chance at resisting the Thalmor.
In terms of character, I think Ulfric is a bit scummy. Challenging a king, who had nothing but respect for him, to a duel he could not win… is quite low, especially if the purpose of doing so was for appearances. Although the Bear of Markarth was written by an Imperial scholar who is biased in favour of the reach, it’s clear that some of what is written there is based on fact, as can be heard from the prisoners in the Silver Blood mine. He’s also mostly to blame for the Civil War, which benefits the Thalmor.
That said, he’s clearly written to be stronger in spirit than Tullius, a mediocre yet servicable leader. As such, I prefer Ulfric to Tullius and the rest of the Empire, and he has been the main reason I’ve traditionally sided with the Stormcloaks on my playthroughs.
On specific points:
Talos worship is important; in the Empire’s defense, it isn’t in a place to resist both the Thalmor and the Stormcloaks.
Ulfric being a Thalmor spy is a meme. Anybody who thinks that is illiterate; the Thalmor consider him an “uncooperative asset”, a far cry from a spy.
The racism thing is irrelevant. The stormcloaks are more ethnocentric, but it’s not like other races in Skyrim don’t have the same attitude.
The empire tried to behead you. So what. Does everything have to be about you?
Ulfric was a bit less reasonable than Tullius in the negotiations, but to be fair to him, the truce is worse for him than the empire.
Tullius is ignorant of Nordic customs, though I don’t see how relevant that is to the conflict.
Saadia vs Kematu
On my first run, I think I spared Saadia, which was a mistake. Her story is more inconsistent with Hammerfell’s history, and she’s the one who wants to escalate the most.
Corrupt or purify the star of Azura
Corrupting is better for gameplay, but purifying is the “right” thing to do.
Which of the three (four?) captives should be killed
I kill the Khajiit and/or the woman. The woman is obnoxious and the Khajiit is the one who is most likely to have a contract on his head.
Dawnguard vs Vampire Lord
The vampire lord is lame and ugly. As such, I always side with the Dawnguard.
Faendal vs Sven
Both of them suck. But Faendal sucks less.
Cure lycanthropy
Do it. Being a werewolf sucks.
Spare or kill Cicero
On my first playthrough, I killed Cicero, and felt guilty about it. He was insane and tried to kill three of my colleagues, but something about killing him felt off. As such, on further playthroughs, I spared him. Later, I read his diaries and found his story sympathetic; that alone made me not want to kill him. Then, I learned that Lucien Lachance claims Sithis doesn’t want him to die.
It’s pretty obvious from the lore and dialogue that Cicero is not supposed to die.
Spare or kill Paarthunax
Obviously spare. Fuck the blades.
Spare or kill Madanach
Kill. Fuck that guy. His followers in the cell seem alright, so I let them live.
Spare or kill Barbas
The axe Clavicus gives you sucks. May as well spare Barbas; the Helmet is way cooler.
Spare or kill Sinding
Spare. He did nothing wrong.
Spare or kill Motierre
Not much information to go on here. I lean towards spare, since the Empire’s mediocre leadership is a reason to side with the Stormcloaks.
Good choices all around. I think the Nords would likely assist the empire in the event of a Thalmor invasion, but would not assist the Empire if the Empire sought to invade Valenwood. The Redguards wouldn't assist the Empire at all, they are basically Elves in their religion (anti-Lorkhanic). Not a fan of the Greybeards but I agree it is treacherous to kill Paarthunax. Madanach deserved to die and so did his followers. No sympathy for Reachfolk, they're just the worst.
I supported the Stormcloaks, but the issue with "sacrificing the Empire for Skyrim" is that the Thalmor are so powerful that humans really sort of have to be united against them. The Altmer are taller, more intelligent, longer-lived, and much more magically adept than humans and even the Imperial Battlemages. Their fleet is very strong too. Skyrim is kind of a dilapidated shithole by the time of TES 5. If the Altmer re-established control over the heartlands Skyrim would quickly fall next. Maybe the Dovahkiin could do something to stop it? Maybe. He's not a god. And the Thalmor can just wait until he exhausts his tiny human lifespan. The one thing humans have in their favor is that the Altmer kind of have a birth rate crisis.
Sven sweep