Mouseferatu
Hero
Did they say Enterprise was the Starfleet flagship? IIRC, in the original series/timeline, it wasn't the flagship until after Kirk & co. covered it (and themselves) in glory a few times.
Well, that and the fact that in o/canon (that is "original canon," as opposed to n/canon, or "new canon"), it was the only one of the original 13 Constitution-class cruisers to survive up into the movie timeline.
Yes, Pike referred to it in the movie as the "new flagship." But whether he meant it was the new flagship of the entire fleet, or just of the cadet-driven "mini-fleet" that was dispatched to Vulcan is, I suppose, arguable.