Alonso and Rosberg and to a certain extent Kimi are the only drivers I can think of this season who "outperformed" their cars.
yes, you are right.
Hamilton has made a "normal" season for me.
1st part of season with a c**p car : he has made many errors (China 09, Monaco 09, late braking Nurburg 09, ...) and he shows he has no personnality (Australia 09).
2nd part of season with a very good car : he has made some great quali lap but he was not so exceptionnal on race.
Hamilton was in 2009 like Alonso in 2008 : a c**p car in 1st part of season, and a excellent car in the 2nd part of season.
But in 2008, Alonso was better than Hamilton in 2009 in the 2nd part of season, and in 1st part of season, he has made some exceptionnal performances (Australia, Spain, ...) contrary to Hamilton in 2009.
Alonso has made a great 2009 season : he has got a c**p car during the whole year and he has made some great performance (Suzuka, Malaysia, ...) but he was at the back of the grid and few people saw he made some magic drives.
Kimi has made a great 2nd part of the season with a c**p car (remember he can have play the victory in Brazil without an very unfair move of Webber).
The problem is that Massa wasnt driving and we dont know if Massa could have make better than Kimi.
Rosberg has also been very good, but like Alonso, he was often time in the back and many people didnt saw his great performances.
Also, I think Kovalainen is a very bad driver : he has no personnality (I remember Hockenheim 2008 when he let Lewis pass without any team order) and he has made some very c**p races (Australia, Malaysia, Monza, Valencia, ......).
To conclude, this season was strange with nobody in top 3 (rubens, vettel, button) who deserve the WDC.