Hamilton is a beast at Qualifying, of that there is no doubt, but if he had better race craft and didn't let his emotions run away with him he'd be almost the perfect racing driver.
To be the perfect racing driver, Hamilton would have to increase his intelligence. That's not easy. Because of this he relies on his teams telling him to make the strategic decisions, while he does what he does best - drive fast.
For me Vettel and Alonso, with their higher intelligence (and better decision making during the race), will beat Hamilton over the course of a long title race.
If you look at the best drivers in history - Senna, Prost, MSc, Alonso, Vettel (but to name a few) - they certainly have speed. But they also have intelligence. And this is always going to hurt Hamilton, when it comes to putting multiple titles together. We have seen this already.
This year, we are seeing a slower driver, with higher intelligence, leading the title race. It could certainly be argued that Hamlton had a DNF which hurt him in Race1, BUT, I would argue that if Rosberg were falling behind too far, he would've pulled a rabit out of the bag sooner. Some people call it cheating. I call it F1.