Trump made the same mistake GWBush made. He left too many NSC and State Department staffers in place, wrongly thinking his chiefs would lead and be in charge, while those staffers, part of the deep state, think that they, not the elected officials make (or ought to be making) policy.
As I’ve said before ... If President Trump only put trusted people in those positions, then about 95% of the leadership positions in the executive branch of the U.S. government would be vacant. And most of those that COULD be filled would have a Trump family member in it.