C.E. Evans said:
Perhaps the term "expeditionary fleet" can be used to describe several exploration ships answerable to a single admiral. These ships could all be on separate missions in different regions of space within a quadrant or sector...
That's how I've always imagined it. Someone like Commodore Wesley or Decker would have been the senior officer of the local exploratory group during Kirk's 5 year mission even though the ships generally operated independently. Each group then would be a part of a larger force, perhaps a fleet, under the command of a Rear-Admiral.