Enterprise as training ship followed up with it ready to be decommissioned in TSFS.
If the '09 movie presented one good idea for the structure of Starfleet, it was that a Captain might be training cadets on a ship to later be his crew on that ship. In that movie, Pike is training cadets on the then-new Enterprise who will actually be his crew on that Enterprise. I assume that this writing suggests the writers have the same impression that I got when first watching Star Trek II.
When I first saw that movie, my impression was that the Enterprise was not a "training ship," but was in fact going to go on duty at some point, with a mostly new crew that Spock was training. This is because McCoy asks if it would not be better to "put an experienced crew back on the ship." Probably many of the other officers are going on to other positions, especially since most are full commanders or above at that point. Would Saavik have been Captain or was she getting officer training to be Spock's first officer? I'm not sure.
Perhaps Kirk knows that this time, Starfleet will not let him take back command of the Enterprise, and his line about such missions being "for the young" was a way of mocking his superiors without really saying it. Sometimes a person in authority will say something that clues in the subordinates that the person does not like what has to be done, but they all have to do it anyway. If Starfleet has promotions that relate to age (or better-stated, years of experience, since Kirk was supposedly a young captain during TOS) perhaps Kirk would be seen as now having been in the service to many years to be a captain of a ship, and it overseeing this training because it is the mostly like what he wants to do that he can.
Lastly, assuming that for the movies the first two digits of the stardate relate to the year, TMP would be in '74 and The Wrath of Khan in '81. That is enough time for an entire 5-year mission with Kirk as an admiral serving as captain, after which he was compelled to return to administrative tasks.
To my mind, the time Kirk "left Starfleet" shown in Generations, is probably meant to the the time after the 5-year mission that followed TMP, but before Kirk becomes an Academy instructor for Star Trek II.
Taking all that into account I could see TOS, TMP and movies II-VI as being in the same universe, but as shown with Kirk, things would have to happen in between that change how the characters relate to their situations.