I think it's kind of brilliant that gamesas made it so that neither side is clearly a better choice. They both have good and bad things (this list is by no means exhaustive; just what I've noticed so far):
Empire:
* Tries to kill you right at the start of the game
* Tool of the Thalmor (though perhaps would like to shake off the Thalmor, just not strong enough to do it yet)
* Religious persecution
* Weak (as evidenced by the fact that the Thalmor have so much say in internal affairs), perhaps needs to be replaced by a new empire, or by independent states, or by a confedration, etc.
* Well organized, so potetially lots to offer you if you try to work from within to reform the system, instead of from without to overthrow.
* Problems with corruption and incompetence
Stormcloaks:
* Doesn't try to kill you (at least, until you join the Imperials)
* Might be unwitting (or perhaps some at the top are complicit) tools of the Thalmor, keeping the Empire weakened so it can't shake off the Dominion's influence.
* Claims to want to offer religious freedom (although, also seems to persecute the Forsworn, maybe Daedra worshippers, etc)
* but is also very racist/Nord Supremecists.
* Weak and disorganized, though potentially can grow in strength with the right Hero aiding them.
* Their civil war, even if justified, means a lot of people are going to die.
* May achieve independence from the Thalmor and Empire, but in fracturing and further weakening the Empire, may sow the seeds of Tamriel's downfall and their own destruction.
* Problems with corruption and incompetence
So, in the end, the player gets to choose based upon what's most important to them. I didn't at all feel pushed towards the empire - I kind of resent that they wanted to give me a craniectomy, and despise the Thalmor, so I chose the Stormcloaks, but I did wrestle somewhat with the decision. The OP, on the other hand, because different things were important to him/her, thought they were lead in a different direction for their choice. That tells me the writers hit almost a perfect balance if different people feel the 'natural choice' is different.