The depth of the NA teams at i46 were much better than HRG's at i49. That's not to say that Europe didn't prepare better with rosters and game-plans.
Sure, I think HRG was thrown off just a little bit by going from QF to the traditional style in less than a week, but the former reason I mentioned had much more to do with it. In fact, I still think the result would have been the same even if the QF never existed.