If you start handing out $50,000 commissions to major artists, there’s not a lot of excuse for coming up almost completely empty-handed at the end of a decade. Muhly’s “Two Boys,” which began under the program’s auspices, made it to the Met’s main stage; everything else was either rejected (like Rufus Wainwright’s “Prima Donna”), fell through, or simply withered on the vine, and no new blood has been added to the pipeline for years.