Basically, it's the only issue on which UFP SF really dares differ from USN. As such, it undermines the idea that alien rank systems could be translated in terms of the "human" one; if the humans haven't managed to "standardize" their own system, then such translations would become quite futile. (I might buy there being a standard translation where the starting rank each culture prefers for the CO of a ship gets called "Captain", but it would be weird to call an ill-defined alien rank "Major" unless one could find direct parallels, a six-step line officer scale and so forth.)
Timo Saloniemi
But Trek never suggested alien ranks were so easily translated. The Romulans had ranks of Centurion and Sub-Commander with a rank of Commander that seems to correspond more to Captain or Commodore. We never get a fix on what Klingon ranks were in TOS: Koloth is a Captain, Kang is a Commander and do we ever find out what Kor was? And this is long before the Ferengi with their Daemons and the Cardassians with their Glins, Guls and Legates.
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To avoid confusion between Pike's rank and position, Kirk would thus emphasize the former by adding the seldom used specifier "Fleet". Kirk could have applied the same specifer to himself if he wished, or addressed Mendez as "Fleet Commodore" (perhaps to distinguish him from a convoy commodore or from a civilian with the title Commodore), but there was no corresponding need for that at the time.
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Sort of like the academics will say "Full Professor" to imply that you don't have those pesky adjectivers like "Associate" or "Assistant." Quite reasonable.
Hell, I only have an MA and teach courses for a university that's maybe two steps above a diploma mill. Technically, I'm an "instructor" (a job title that sounds even lamer than "teacher," my day job) but the students call me "professor."