Reporters have said that they've known BB to want to move to a bit more of the Shanahan system for a while, and have opined that Brady was the reason that didn't happen. But, be that as it may, we can see that the Weiss/O'Brien/McDaniels system is still very effective in the NFL, and was good for Jones.
So, while I can understand the idea of being interested in change, it didn't make sense to push it the way BB did, given the QB he has under center. The whole point of the Shanahan system is to make it idiot proof at the QB position, and it only works if you've got a lot of offensive talent at positions other than QB. The strength of Jones is supposed to be his intelligence. So BB effectively drafted a Brainiac and then drew up a "game plan" for a jock.