One thing from an old WoW player, that started heppening only after Burning Crusade. Before that there was a severe imbalance towards Alliance, then the Blood Elves came along and every kid who wish he could be "Legolas" switched sides.
Now, on the topic at hand. It's simple, it's the storylines, the Imperial ones are umpredictable, full of plot twists and you can expect everything from everyone, there's more feeling of real "danger". With the republic, what i saw is that the stories are more straightforward, and that is cool, but at the same time there's less mistery.