The simple fact of the matter is that they didn't have many good games when Xavi was out. Fact. When Messi isn't there, there's always Bojan, Pedro, Villa to score goals. If Xavi isn't there, there's no one to dictate the pace of the game. Simple really.
They really struggled at times last season when Xavi was on the pitch but Messi wasn't. The difference was Xavi pulls the strings for the others, Messi makes things happen out of thin air.