Problem in Pakistan is neither ISI nor IB neither it matters who controls what. Problem is the political system and the way government is run. As long as non-equals would represent the equals and as long as government in Pakistan would be run like it is private property of people governing, nothing would change in Pakistan.
It is possible that wolves rule sheep and police fear criminals, but we should understand that wolves could not represent sheep neither criminals could get respect of police. In Pakistan, most politicians are wolves whom some people may vote but know that they are not really equal to them. When these politicians rule, they expect respect of government employees (civilians or military) not because of their character, morality, principles, hard work, commitment to serve the country, work for people, etc, but just because they are voted in power.
These politicians do not realise that how government servants (military, intelligence, bureaucrats, etc) would respect them and would let them loot and plunder the country peacefully when they know that these people are crooks and thugs in sheep clothing. So, regardless of who controls ISI, IB or whatever government departments, as long as Pakistani political system would send crooks and thugs in parliament whose only purpose in parliament would be to loot, plunder, and work for their selfish benefits, things would never change.