Some people want to stick it to the Dolans, Bloomberg and the NFL among them, for their campaign against the West Side stadium.
But Quinn and Bloomberg don't exactly see eye-to-eye. Her June push for only 10 more years was an independent (and, to many, surprising) move. She argued for this based on heavy popular support; the community, the borough president, Amtrak - a lot of people wanted an even shorter limit. (Also, Bloomberg's term is up this fall and Quinn is certainly going to succeed him.)
MSG renovated knowing that their permit was up for renewal. And they were as aware as anyone that increased density and a renovated Penn Station were higher priorities than maintaining an arena on the site; the renovation was intended to increase revenue in the short term, buying the Knicks and Rangers some time before they have to move. A billion dollars is a drop in the bucket to them; they'll make that back twice over before the decade is out.
Finally, it's not possible to do much of anything to a basement train station with a 25-foot ceiling and an arena on top of it. And the inadequacy of the Amtrak facility is far from the only reason that the Planning Commission wants changes at Penn Plaza.