I think the crusades aren't just lacking a flavor, but in mechanics as well. For instance, Jerusalem shouldn't be annexed by one of the participating kingdoms, but be created as an independant kingdom ruled by a dynasty (AI should just grant independance to far-away lands in general, IMHO). Merchant Republics should have the opportunity to give boats in exchange for a favor (a small one, such as sacking Constantinople on the way).
Jerusalem should go to the most active general in the crusade. Jerusalem wasn't given to some nobody.