Barry Scott Will
From Merriam-Webster
Main Entry: flag-ship Pronunciation: 'flag-"ship Function: noun Date: 1672 1: the ship that carries the commander of a fleet or subdivision of a fleet and flies his flag 2: the finest, largest, or most important one of a series, network, or chain
It is important to understand the two different definitions of the word "flagship." The first is a technical definition, the second a complimentary definition. By both definitions, Enterprise has been or is a flagship, but not the flagship of the Federation. The truth is that there are scores of ships that can be called such.
In the first instance, the word "flagship" is specifically referring to the vessel which acts as the base of operations for a flag officer. A flag officer in the navy (Starfleet uses naval terms and organization) is equivalent to a general in the army. The rank of a flag officer can be Admiral, Vice-Admiral or Commodore. Occasionally, a Fleet Captain rank is given to a fleet commander who still holds the rank of Captain. Flag officers generally command more than one ship, and only rarely do they have direct command of their own flagship. Also, a flagship could refer to the ship commanded by the commander of a fleet, even if that commander is not flag rank.
There are several instances where Enterprise has served as a flagship that carries a flag officer or the commander of a fleet. In Star Trek: The Motion Picture and Star Trek II: The Wrath of Khan, Enterprise is under the command of Admiral Kirk and can be correctly referred to as his flagship. (Star Trek III: The Search for Spock is not relevant as Enterprise is not fully crewed and Admiral Kirk is violating Starfleet orders.)
In the TNG episode Redemption, Part II, Enterprise-D is Picard's flagship as he commands the small fleet that prevents the Romulan incursion into Klingon space. In Star Trek: First Contact, Enterprise-E is briefly (about 2 minutes) the flagship of the commander of the fleet fighting the Borg cube.
Under the technical definition of flagship, there are dozens of flagships in Starfleet. Starfleet has, at minimum, several thousand ships. Each separate fleet or subdivision of a fleet has a flagship. Additionally, groups of fleets will have a flagship. While Enterprise has occasionally been a flagship, it is not a permanent position. Enterprise does not normally serve as base of operations of a flag officer nor for the commander of any fleet. Therefore, Enterprise is not normally a flagship of the Federation.
As a compliment paid to the "finest, largest, or most important" ship in Starfleet, Enterprise has been referred to as the flagship of the Federation at least three times. In the TNG episodes Drumhead and Sarek, and in Star Trek: Generations. In each case, this reference is either a compliment (if coming from a visitor) or a boast (if coming from a member of the crew). It has no meaning other than that Enterprise is considered to be the best of the best.
Of course, with a total size of thousands of ships, there are probably many other ships in Starfleet that could be referred to as flagships of the Federation. As an analogy, consider the Heisman Trophy. This award is given to the "best athlete in college football" each year. Last year, this award was won by Charles Woodson. He is the Heisman Trophy winner. But so is Danny Wuerffel (1996 winner). And so will this year's winner be the Heisman Trophy winner. Each is also a Heisman Trophy winner.
Of course, winning the Heisman Trophy does not necessarily mean that one is the very best player in college football. It is purely subjective and means nothing. Desmond Howard, Charlie Ward and Gino Torretta are all recent winners who have not had much success in the NFL. In much the same way, referring to Enterprise as "the flagship of the Federation" is merely a nice way of complimenting the ship and her crew for their achievements.
In short, if you wish to consider Enterprise as the flagship, feel free to do so. No one is stopping you. However, keep in mind that this designation means absolutely nothing. There is no special function served by Enterprise nor is it technically a flagship. Also, there are dozens of other ships that can claim the same distinction. In my personal opinion, this particular word is one that is merely thrown about by writers who do not truly understand its meaning. But again, that's just my opinion.
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