I meant to add that I have thought all along that Bush wanted Roberts as Chief, and would have moved to elevate him had Rehnquist lived until Roberts was confirmed as Associate Justice. This just messes up the timing a bit.
I don't think Scalia wanted to be Chief. I won't be surprised to see him retire after this term, and he would have been obligated to stay on for life if he had been made Chief. Plus he knew the confirmation process would have been bloody and exhausting for him.
It also means that Gonzales will not be nominated for the position of Chief Justice. I have severe reservations on him.