A true prequel would be an absolute minefield continuity wise and would likely have had to span a substantially longer period than Trek IX to facilitate the meetings of all the characters.
And would have left the "new" STAR TREK movies in the middle of the continuity minefield for every movie to come. "Wait? Why isn't Kirk serving on the Reliant
now? Why isn't he dating Janice Lester . . . or Carol Marcus . . . or Ruth . . . ? What about the gas monster from 'Obsession'? Where does Kodos the Executioner fit in? Why is Chekov on the bridge already? Where is Dr. Piper? And Robert April?"
Like I said before, better to tear the "Canon" bandaid off in one clean swoop, rather than get nitpicked to death, continuity-wise, for the next ten years . . . .