You totally lose me there.  Just because it was among his last doesn't make it his best.  And I would hardly call it a "masterwork".
Every time I see it I get so jazzed up, and excited, because...MUPPETS.  MUPPET THEATER!  The pre-show is a delight.  I enter the theater all ready for some Muppet action.  And then, the film starts, and then I remember...oh yeah, the Muppets are only in a few minutes of the film, it is a horridly outdated concept (so much so that it is probably very confusing to anyone under 20 yo), the 3D is remarkably bad, and the idea of "Waldo" as a Muppet is no more accurate than calling any CGI character that is motion controlled by a human a "Muppet".
I leave with a heavy heart every time that this is the best we get for them.