I suspect that the intelligence apparatus is so influential across the administration that it's very hard for the President to rein it in.

Obama has had to make compromises on which issues he's going to push for. The disappointingly slow progress on Guantánamo Bay was an example of this... And that's a single prison camp with a relative handful of people in it. Digital surveillance is an out-of-control monster that all branches of intelligence just want to have more of, as evidenced by this latest decision on data sharing.