The Nobel Prize in Literature always has been and likely always will be a controversial category. No doubt any book-lover can name a handful of authors that ostensibly deserve the honor, but there are a lot of great authors and only one Nobel Prize per year! For what it's worth, Pynchon is notoriously reclusive and not the kind of person who's likely waiting for the spotlight that the Swedish Academy would be shining. As things stand, the film adaptation of Inherent Vice seems to bring promise of greater attention to his work that it has received in a while now.
I suspect that is a big part why he didn't get the prize and probably won't in the future. If I remember correctly, the Nobel prize commitee was already kind of annoyed that Elfriede Jellinek did not come in person to receive her prize, and Pynchon most likely would not even send a video message.
That, and the fact that there are, of course, lots and lots and lots of breathtakingly great writers out there. I've had the feeling over the past couple of years that the Nobel for literature was often given to authors the commitee felt deserved more attention.