I think Goodell is hell bent on making sure that classic pocket passers thrive, as he is undoubtedly noticing the trend that mobile, less "marketable" players are taking over the QB position in the NFL. He wants folks like Brady, Manning, and Brees to be the face of the NFL, not necessarily, Wilson, Kapernick, Manziel, etc. Goodell is a marketing guy and I suspect that is where he is coming from.
The problem he has is the NFL can only take what colleges give them. Now, the top QB prospects are increasingly mobile guys. The top 4 QBs for next year's draft are Winston, Hundley, Marriotta and Petty, all mobile guys (don't let Petty's skin color fool you, he had 12 rushing TDs last year).
It is just annoying. He's trying to hold back the game, and now, a scrub off the street can pass for 3,000.
A part of me wants Manning to throw for 8,000 yards so people can see how absurd this is getting. The NFL is now a cross between the CFL and Arena football. Goodell has to be the worst commissioner of all time.