I agree that crusades are a bit...weird.
As far as I can tell so far, the mechanics haven't changed much between KoH and KoH2:S, but as far as I can tell, the influence you have on them as a player has actually decreased.
I have only done a crusade once so far (the Pope has the nasty habit to always ask at the most inconvenient of times ), so this may not be representative.
I was playing as the Teutonic Knights and the crusade was against Yemen. So my guy walks then sails all across the map to the southeast, lays siege to a town (Ascalon) and even wins without me sending any additional troops to help (this rarely happened in KoH because crusader forces were almost always too weak on their own).
Now what would have happened in KoH, if memory serves, is that the game would ask me if I wanted to create a vassal state, and then the crusade would have been over.
What happened here is, my marshal did not ask me what I wanted to do, he just gifted the town and province to another (!) muslim (!) state (Akkon), then went on his merry way to the next town, where, with his now much diminished forces, he got his butt handed to him.
I was... suprised.