I really feel Felipe Massa never fully recovered from his injury in 2009, a look at the stats should support this.
In 2008 he outscored one the best drivers on the grid in Kimi, yes it was Kimi's worst year of his career but it takes at least very good driver to beat a off-pace great driver. The year earlier in 2007 which was one of Kimi's best years, he scored respectfully and around 85% of the points Kimi scored. The Ferrari of 2009 was a bit of a hound dog, but before his crash he was outscoring Kimi in the standings.
Now, this is not to say Massa was performed better than Kimi when they were teammates, but to be this competitive and to outscore Kimi in the time they were teammates over 2 and a half seasons for me is definitive proof that Massa was a world class driver and WDC contender material.
We all know Alonso is a great driver, and a large portion on the fanbase tag him as the best driver on the grid. But you would expect from the results Massa produced against Kimi in 2007-2009 for Massa to be closer to Alonso than he has been. Alonso doubled Massa's tally in 2011 and 2012, and Massa was only able to score around 60% of Alonso's points in 2010.
Is Alonso really that much better than Kimi? I would say no, Alonso I think is a better driver, but not to the extent the difference in teammate head to heads show.
I believe Massa lost something from that crash that he has never recovered. It is a shame because before his crash, he was a really good driver, on par with Button and in my opinion better than Mark Webber has ever been.