Weren't there no Lieutenant junior grades in TOS too?
Naah. There was even a specific rank braid for Lt(jg) in TOS: a single broken braid, when Lt was solid braid and LtCmdr was solid and broken. Lieutenant Joe Tormolen in "The Naked Time" wore the broken braid, even if nobody called him Junior at his face. (Or perhaps somebody did, and that's why he committed suicide?)
It was just that Ensigns in TOS had no rank braid to separate them from assorted enlisted personnel. So in ST:TMP, it was decided to assign the one broken braid to Ensigns - a silly decision that in theory banished Lt(jg) from existence. But happily, nobody in TMP came out and said to the camera "Ensigns now wear broken braid and there are no Junior Lieutenants". At worst, we got a single line where a person wearing broken braid was referred to as Ensign - and, as with so many little incidents in TOS, we can claim that the person speaking was making a mistake, forgetting the other guy's recent promotion...
It would be rather odd for Starfleet (UFP or UE) to suddenly go and abolish a rank for a period of a few decades, then reinstate it, when the Starfleet rank system otherwise is based on the USN one and would seem to have a very stable and continuous history. It's much easier to believe that we just failed to meet the wearers of some specific rank.
Say, the Mercury astronauts were all officers from USAF, USN or USMC. Of the Navy guys, Shepard and Schirra were LtCmdrs but Carpenter was a Lieutenant; all the USAF pilots were Captains (the same as LtCmdr); Glenn, the only Marine, was a LtCol (the same as Commander). Since they were all hired to do the same job, we might speculate that USAF doesn't have any Lieutenants since their guys don't show the variety the USN guys do. Or we might decide the USMC skips Captain (that is, LtCmdr) rank because why else would Glenn be justified in being higher-ranked than the rest of the bunch? But a selection of seven heroes isn't statistically enough to make such conclusions - and seven heroes is what we generally get in Star Trek shows, too...
Well, even the ranks of the US Navy have changed over time... in the case of the flag officers they even have jumped back and forth.
Ensign: Replaced the rank of "Passed Midshipman" in 1862.
Lieutenant (junior grade): Replaced the rank of "Master" in 1883.
Commander: Replaced the rank of "Master Commandant" in 1838.
Commodore: Was abolished and re-established several times throughout the 19th and 20th centuries. Replacements include the ranks of "Commodore Admiral" and "Rear Admiral (lower half)". Often the rank was abolished altogether. First established as a rank in 1862, last abolished (or replaced) in 1983.
Rear Admiral, Vice Admiral, and Admiral: Gradually established as ranks between 1862 and 1866. The admiral ranks subsequently fell into disuse after the civil war and were not re-established until the two world wars.
Fleet Admiral: Established in 1944, fell into disuse after World War II.
Originally, there was no naval rank between "Captain" and "Lieutenant" at all. Lieutenants were usually promoted to Captain right away.
The general rule seems to be: The fewer the ships and the smaller the navy, the fewer the ranks. So you could make indeed make an argument that there no "Lieutenant junior grade" and "Lieutenant commander" ranks in the 22nd century. In the beginning there was only a single (later two) warp 5 ship and a number of smaller ships like the Intrepid.