While it will never be proven, I still say John Harbaugh was the one who initiated all of this. He whined about the Pats creative use of the eligible/ineligible receiver rule, so Brady responded with his "study the rulebook" comment.
I know Ryan Grigson and the Colts were the ones to initially email the league about their concerns, but both Grigson and Chuck Pagano originally came from Baltimore and worked with Harbaugh. They're buddies and both hold a common disliking for the Patriots. As soon as Harbaugh heard the "study the rulebook" comment, I think that got the ball rolling on all of this.
Even the email sent by the Colts to the league specifically said "We, along with many other teams, widely believe they've been doing this for awhile." Well if it was going on for awhile, why wait so long to mention something?...That rulebook comment I really think has started all of this.