I see it this way:
I feel that Hamilton was much better with the '08 spec cars. He made some crazy moves, and they typically paid off. At that point in time, he WAS the BEST driver on the grid, no doubt. If we had kept the same regs, I think Hamilton would have had a great chance at the "Hat Trick".
When they switched to the Current aero rules, I think he found the car not to his liking. Less rear grip, and making a pass move was much easier, and thus, more expected. People saw him about to make a move, and would adjust accordingly. Throw in that the McLaren was a dog in '09 and part of '10, he wasn't able to keep pace with people who were up the field.
Hamilton seems to put it all on the line, and the Tyre Gods punish him for it. If you took tyres out of the equation, I think you would find that Hamilton has the best race craft, and could set the quickest lap time.
Vettel, on the other hand, seems to have a good grasp on knowing what sort of lap times he needs to set to bring the Tyre/pitstop strategy on his side, and use that to his advantage. He seems to be very calculating, and very precise.
Few times have i seen Vettel make a sensational move on someone, or make a pass in a place one would not expect. He races fairly conventionally, and that can swing in his favor.
However, I feel that in a Sprint race, say 5 laps, him and Hamilton in the same cars, Hamilton would have him. Vettel gets more luck on overall strategy, but in short blasts, I feel that noone can touch Hamilton. Vettel is gifted, just not in raw speed.
Another issue Vettel seems to have is when his back is against the wall, he slips up. (Canada, Spa) He goes harder than he and the car are capable of, and spins. Hamilton, in my eyes, when he is in a low place, can put in a stellar stint, and pull off what few thought he would.
I don't think there is a definitive answer to this, but all I can say is I'd love to see Lewis and Seb in a round of the BTCC. That would be great to watch.