FBI and CIA Merger
The FBI and CIA should be merged into one intelligence agency. They are both involved in intelligence gathering, and it would a make more sense to organize them as complimentary subsets within one intelligence organization than as completely independent organizations, especially in this modern world where the boundaries between wholly domestic or wholly international activities are increasingly becoming blurred. This would also encourage the personnel of the two organizations to communicate more effectively with each other.
Authorization to Kill
Neither organization, because they are civilian, should have the authority to assassinate or kill anyone. Both of these agencies, as would any law enforcement agency, have, as their primary purpose, the gathering of information. They should be fully empowered to arrest and transport individuals, using whatever force is necessary, where ever in the world they may be (with proper justification) and interrogate them. The killing of hostiles is naturally sometimes necessary for self-defense. However, capture and trial should obviously be the top priority. The military is the organization that should be responsible for an actual targeted killing. Such military actions, however, would need the authorization of the civilian command and control structure so that civilian control and oversight is maintained.
It is very important that a single organization does not possess both the power to develop a comprehensive intelligence (as the CIA possesses) as well as the power to deliver functional military strikes. Otherwise, the organization that has both capabilities can have too much leverage against the other arms of government, leading to an increased chance of destabilization and weakening of the proper civilian oversight and control. Not only could this lead to an ill-informed citizenry, but could also potentially lead further down the road to a coup d’état.