Geordi's use of the phrase "The flagship of the Federation" was correct when referring to the NCC-1701-E in Star Trek: First Contact because the Sovereign-class Enterprise was the most advanced at the time.
Flagship can also be used to refer to a ship when it is the lead ship in a fleet of vessels, a designation given on account of it being the largest, fastest, newest, most advanced, most heavily armed or, for publicity purposes, the most well known.
Okay, you're quoting the bolded portion directly from Wikipedia's "Flagship" entry (or rather, you're plagiarizing it -- in future, don't quote something directly without citing your source, please). But that's not always the most reliable source, and I think it's conflating multiple different uses.
From the OAD:
the ship in a fleet that carries the commanding admiral.
....• the best or most important thing owned or produced by a particular organization
In strictly military terms, I think Babaganoosh is right -- a flagship is the ship on which the commander of a fleet (whether a group of ships operating jointly or simply the navy at large) is based.
The US Navy sometimes uses the term "flagship" in the context of competition or recognition of excellence, wherein the group which wins the competition or is otherwise recognized for excellence is designated the "flagship" within certain contexts. I don't think the civilian usage of the term is entirely foreign to the sea service. If anything, usage seems quite parallel.
Steve Mollmann wrote:
That said,Enterprise is Starfleet's flagship not for technical reasons,not even because an admiral commanded one,but because a ship called Enterprise has been around before the Federation even existed.In homage to that history the Enterprise will always be the Federation flagship.
I suspect there's more to it than that, otherwise Kumari
would be the flagship.
Put differently, one might conclude that the unique role of Enterprise
in the Federation's formation (perhaps
coupled with the previous history of ships of the same name) might have garnered it a permanent place of honor.
Santa Claws wrote:
I think, even though the Aventine is one of the largest and one of the most advanced ships of the fleet, it does not really have a long history like the Enterprise has, that should count a bit.
I like both views of a flagship -- a vessel representing the vanguard of the Federation and a vessel carrying the flag of a commanding officer of a fleet. Of course, in "Star Trek," we never really saw a lot of admirals or commodores commanding from single starships (although we did see Admiral Hansen in the "Best of Both Worlds.").
I view Aventine in a light similar to the original Excelsior. The Excelsior was outfitted with transwarp engines and was touted as the future of Starfleet (much to Scotty's chagrin). Only after the experimental stuff was removed and the ship was allowed to prove itself did it become the vanguard of the fleet (as evidenced by the longivity of the Excesior-class).
Did the Excelsior eventually become a "flagship?" Yes, I believe it did. The Federation is big enough to have multiple explorer-type ships carrying its banner (or flag) to the edges of the final frontier.
Wasn't there some supposition that the Excelsior
was designated the Flagship between the decommissioning of the Enterprise
-A and the launch of the Enterprise