Certifiably Ingame tackles what it means to be the flagship of the fleet.
The biggest thing that occurs to me is "why are we sending the flagship out past the known Federation for a years-long mission of exploration?"
I mean, really. And this doesn't even apply to just the E-D, but the 1701 as well. Kirk's ship seldom hung around the core of the Federation.
Then again, Trek never really used the term "flagship" correctly. It's supposed to mean the lead ship of a fleet, the one that figuratively flew the admiral's flag. The only time that I recall the Enterprise even serving as the key member of a fleet, admiral or no admiral, is First Contact. Even the Battle of Wolf 359 had the flagship be the Melbourne under Admiral Hansen.
In a loser sense a "flagship" could also mean simply the most advanced or important ship in the general fleet, which would fit the Enterprise, except when it doesn't. Sure the refit 1701 was the most advanced for a time, but they were quickly supplanted by the Excelsior class. I even think that the Galaxy class didn't hold the title very long after the Borg invasion.
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