I think having separate services is a good idea but I also think that combining the civilian departments (Department of the Army and Department of the Air Force) into a single department might help (similar to the Dept. of the Navy covering both the Navy and the USMC). So we would be left with a Department of Defense and two subordinate departments - the Department of the Navy and the Department of the Army and Air Force. (I also think this might save money.)
They already did in 1947...it's called the Department of Defense.