I'm incredibly impressed with how much Cam improved as a passer from game 1 forward. Still, he's as much a product of Malzahn's system as Luck is of Stanford's. Newton obviously has the intangibles that will give him a leg up on most QB's but we all know he won't be running and scrambling in the NFL with 1/4 the success he has now. People like Karlos Dansby will hurt you.
Someone correct me if I'm wrong here but my feeble analysis of the difference in a "system" QB and what you have to do in the NFL would be having to survey the field. What I see in Cam and Luck and those like them, is pretty much knowing exactly where you're going with the ball on 90+% of your throws. You take the snap and play action or in Cam's case, take the quick step forward to fake a run and then hit the designated receiver. Certainly, there are plenty of cases he has to pull it down or find the 2nd option but for the most part, receiver #1 is going to work...or not.
In the pros, it seems these guys have to have the ability to quickly check options 1, 2 and 3 and pull the trigger. A lot more reading of defenses etc. I have no idea if Cam is there yet or has the ability to do it at that level with one year of D1 experience. Have no idea. I know I probably simplified that too much.