Statistically, we have no particular reason to think that the use of Commodore in Starfleet would have been discontinued. We last heard of one in ST:TMP, after which we have seen up close about a dozen Vice Admirals and just a couple of full, four-pip Admirals in the regular timeline, plus just three two-pip Rear Admirals. In addition to these, there have been unclear cases: lots of background flag officers in the other TOS movies (with very difficult-to-identify pins; many don't even realize Kirk is supposed to be a Rear Admiral), and then these folks in early TNG who wear either zero, one or two pips.
A single-pip Commodore could easily have slipped through the cracks. Or we could have seen several in focus in early TNG, and it's just customary to address all flag ranks as "Admiral" even when some are Commodores and others are Vice Admirals.
Similarly, we have no real statistical reason to think that Lt(jg) or LtCmdr would have been omitted from UESF ranks in ENT, even though we never saw anybody wear those particular rank pins...
It's a bit more complicated with Lt(jg) in ST:TMP, because we did hear not one but two of the heroes address a dashed-braid person as "Ensign" despite said braid that matches that of Lt(jg) Joe Tormolen from TOS. Of course, we could argue that our heroes were out of the loop and unaccustomed to the promotions these people otherwise familiar to them had recently received... But it doesn't seem as if Kirk really knows the "Ensign" he stops at the corridor to ask for directions.
As for Fleet Captain, this title is only used once in all of Star Trek, for Chris Pike's immediate pre-TOS status - so if it ever were a rank, it may have disappeared before TOS already. It might also simply be the very same thing as Captain, though (the "Fleet" thing differentiating the likes of Pike and Kirk from the likes of Mudd and Yates).