Honestly, having done both, their quest lines are eerily similar in terms of what you wind up doing.
In making a decision just base it on what limited amount you know about either. If you listen in on their conversations they're having with their second in command, you'll get some info, and also talking to them about the civil war will also enlighten you on what they feel their positions are.
If you want to get a bonus amount of education on certain elements of the civil war, do the main quest first, at least, through the Thalmor embassy part. This I think might influence your decision. If you don't plan on doing MQ though (have to do some of it at least in order to get to the Battle of Whiterun for either side), you should find sufficient enough talking to Ulfric and Tullius to make some sort of decision based on your own preferences/biases.