As far as how Tebow's throwing ability stacks up against other college perceived by the public to be top prospects, I'd say his arm is no worse than Colt McCoy's. In fact, it's probably better. Tebow's not up there with the Locker's or Snead's, but he's not a total Jason White clone either.
Same goes with the "system" argument against Tebow - neither Sam Bradford (whose draft stock is actually falling fast) nor McCoy play in a pro style sytem either. Therefore, while there is merit to the argument, I don't think it will totally kill his draft grade.