Michaels gearbox broke down and he didn't qualify at Brazil, thats another misleading statistic.
Over the year of 2006 as a whole Michael was drastically faster.
Just like Alonso sometimes falls behind Massa on pace for a few races, it rarely lasts.
Massa's average finish in 2006 was 4.4 and MSC was 2.6. Comprehensive. But given Alonso was 2.0 and Fisi was 4.6, Massa wasn't completely destroyed.