You're forgetting that there was no lieutenant junior grade rank in TOS -- it went straight from ensign to lieutenant. And commodore was evidently phased out sometime in the movie era. So there's already precedent for Starfleet changing its rank structures over time.
Christopher, I agree with your basic premise in this discussion, but I just want to differ slightly with you on this point. There was an apparent Lieutenant Junior Grade rank in TOS, as evidenced by the broken braid on Joe Tormolen's cuff in "The Naked Time." We know that Ensign denoted by no braid (see Chekov) and a solid braid signified Lieutenant (Uhura and Sulu). There would appear to be some grade between the two:
EDIT: I see Avro Arrow
beat me to it!