That would be a major piss off if Vaughn and Syd were set to cross paths in order to fulfill the prophecy. However, prophecy or no prophecy, this is not necessarily true because pretty much everything that has happened in the show was caused by a catalyst that was someone's choices. Back in season 1 (oh, the memories!), Syd could have had another handler instead of Vaughn. She, however, didn't like that guy because he was a major jack ass and made the choice to get rid of this guy. If that never happened, this theory would be a total waste. Although, mind you, the entire plot would be different too, so.... I'm just gonna shut up now and stop theorizing.
Off topic, but ever notice that pretty much everyone here says something in Alias pisses them off but they can't stop watching all the same? I love it!