My Turn to re-spark some discussion. I'm not Pro either of the groups, but I see a lot more flaws in the Rebellion than I do the Empire. If they lacked these flaws, then I would more than likely be Pro Stormcloak, but like I said, I'm nuetral.
1. Racism - Quite possibly my go-to reason to dislike the Stormcloaks. Though not all of them have a blatent hatred towards all Non-Nord races (mainly Mer), but easily more than half of them do. I feel like they would get a lot more "Bees with Honey" if you know what I mean. There are a lot of Mer who aren't pro Thalmor or Empire at all, and I think any ally could help in their cause. This ignorance, and Superiority Complex that most of them suffer could inevitably be weakening their powers.
2. Mis-Understanding History/Lore - The Stormcloak beleif is that the surpression of their Main Diety (Talos) is the biggest offense on them, as well as the Imperialistic Control of the Empire. But Mainly, they use the Worship of Talos to their advantage. This would be correct, if they weren't using this incorrectly. Talos isn't just a Divine for the Nords and Skyrim, but for the Imperials and the Empire as well. He wouldn't have even "become" a Divine if it weren't for his god-like service within the Empire itself. Why would he approve of "his children" fighting his brother and sisters of the Empire? If anything, the Stormcloaks shouldn't even be fighting the Empire at all, but mainly the Thalmor. They would get so much farther if they worked WITH the Empire than against them. But then again, this wouldn't be a Full Blown Rebellion, rather than an Opposition towards the Bullplops Thalmor and Dominion.
3. Use of Force - Think about how much farther they could get with a more Diplomatic approach. Assuming that they had one. They have so many allies with them already, that they have a cockiness that gives them a self-entitlement that all Nords have to support them. If they don't, they become aggressive, like in the case of Whiterun, an Imperial Supporting Hold. If they had simply said that they only wish to protect the city from the Thalmor and their Justicar Thugs, so that the Worship of Talos was allowed, and that they weren't against the Imperials, they could've taken hold of Whiterun, and maybe, slowly swayed the city into Stormcloak Support. (All assuming that Balgruuf isn't being a stubborn ass).
Feel Free to counter argue. I am willing to have a nice discussion. However, don't take offense to me. Remember, I am not a Pro Empire Either. In fact, I could list their issues as well, but I have no time sooo...