Well... there SORT of is...^
^^
^^^In my personal attempt to reconcile the use of the "Delta" as the insigia for Starfleet Command with TOS, I like to think of it in this manner:
The "Daisy (flower) Insignia" was worn by starbase personnel and was NOT Starfleet's insignia. The official insignia for StarFleet command was the "Delta Insignia", and IF the Enterprise was the flagship of the fleet, then it adopted the "delta" as its own. So it was the Enterprise that took the Delta from Starfleet, not vice-versa.
Before you say anything, I realize it is not canon that the Enterprise ever was the "Flagship of Starfleet", but there is nothing that says it wasn't the flagship either.
Kirk, regardless of the fact that he held the rank of Captain, was still a rather JUNIOR captain, during TOS.
Typically, a flagship is not going to be commanded by someone more junior (no matter how CAPABLE the captain may be). In fact, you'd really expect the FLAGSHIP to be commanded by someone with the rank of Admiral. Or, if not Admiral... say, "Fleet Captain?" Or Commodore? (Pike? Decker? Wesley?)
It's really inconceivable that they'd give the FLAGSHIP to the "low man on the totem pole." That is, if Trek is supposed to be something we can watch and suspend our disbelief over.
On the other hand, if you're one of those who says "well, it's all make-believe, so you can do anything you want," well... we'll just say that all pretense of rank has gone away and everybody just thumb-wrestles for command!
