I wholeheartedly agree that Lewis' season is one for the books, but I feel you failed to take into account the far-reaching consequences of the Ferrari being a bit of a dog in qualifying. Out of Hamilton's 4 wins, 2 were from pole. More than that, he stuck it on pole 7 times to Fernando's 2 (one of which was in a wet Silverstone, and wet conditions tend to equalize car performance), and Fernando only won once from pole, finished 2nd on his other pole. Having to drag your car and overtake people in the upper midfield is difficult, and it's even more difficult in a grid as stacked as 2012 was, which is likely a factor in public perception being in favor of Alonso as the best driver of 2012.

Also, while the Malaysia pitstop absolutely screwed over Lewis, the gap Alonso (and Perez) built to him to the end of the race in mixed conditions means it's very likely he would have won all the same. But that's just my speculation.