The Imperials are the example of bureaucracy left unchecked and a military stretched too thin. The Stormcloaks are a bunch of short sighted nationalists who have valid concerns, but are misdirected and manipulated by a ruler who has his own self interest in mind.
The Imperials just want to keep the status quo because it seems to be holding the threat at bay for now, and the Stormcloaks are big mad that their culture is being suppressed by an outside rule. They don't care why it's being suppressed, just that they don't want it to be and whoever is doing the suppressing needs to die.
I wish there was an option for a mutual understanding and unification because either side winning doesn't seem to be a positive outcome. But if I had to choose, I feel like the Imperials would have the resources and direction to get something done if they just got their shit together.