Oh, how I wish there was more neutral options to deal with the Civil War than the game presents you. For instance, maybe the player could act as a intermediary and broker a compromise between Skyrim and the Stormcloaks. i.e. Such as Ulfric being allowed to be High King, but forced to ban public (emphasis on this point) Talos worship, private worship would still be allowed, or maybe an agreement that would allow Skyrim to be made independent of the Empire (thus avoiding the religious issue) but ultimately remain allies of the Empire. I'd the player to have 2 options in completing this route, either diplomatically for the more socially inclined players, or just kick both sides a**es left and right until them come crawling to you to accept the compromise terms for the more combat inclined players (and it would make the player feel like a true badass to be able to pull that off too).
So far, I've stayed out of one side or the other, but purely for tactical reasons once I finally choose a side I'll go Imperial, because both Skyrim and the Empire itself is a LOT more likely to survive or even win a war with the Thalmor if the two sides are united.
I must say that otherwise than the tactical decisions regarding the Civil War, I am very impressed with Bethesda's ability to make this Civil War much more of a grey problem and a challenging decison to make than joining opposing factions in their previous games. In fact, I don't think I've ever come across a dilemma in any video game that's been anywhere near as difficult for me to make as this Civil War.
Except the Thalmor, I kill all Thalmor I meet out on the roads without a second thought. Even if they gave you the option to join them I wouldn't take it in ANY playthrough.
Seriously, F**k those guys.