I think that’s because it would be too obvious to start a MI3a with the same premise you ended MI2 and hold that premise throughout the game/story. That would end up as a predictable, flat story arc. Just look at MI1 and MI2 (or TWP for that matter): none of them end like you would have thought in the beginning or at least the journey in between had some unexpected twists and turns. MI3a would be no different. So in my opinion, it could very well start out as MI3 did, only there they decided to quickly jump ahead to grown Guybrush back in the “real” pirate world and end up again at the Carnival of the Damned, which is pretty flat and maybe why it disappointed so many hardcore canon MI fans.
Another question you should ask yourself: despite being happy there won’t be a MI3a most likely, let’s just assume there will be one in a few years… would you NOT play it? Would you resist just to keep your younger self happy? Or would go “screw you, younger me! Grow up!” and play the game you wanted so long. You survived playing TWP too, didn’t you?
My 2 cents on the real secret: The pinnacle of meta
Note that it doesn’t exclude the possibility that Ron reuses some ideas, including what he had in mind for MI3a.
Also be aware of the historical reality when either MI or MI2 was made: at that time, there was no plan for a sequel let alone a trilogy! Ron could have had a story line in his head, just in case the game sold well and Lucasarts would be ok to do more of these (with him), but unless you have the Voodoo Lady’s clearvoyance powers, you’d better close every game such that the story can exist without a sequel.
The only ones to “blame” for not having MI3a instead of MI3, are Ron leaving Lucasarts and all you guilt-absolved pirating kids back then !
One possible storyline for MI3a -in my mind- could have been a full game where you play Guybrush as a kid in England in the 1970s or 1980s, who’s got a crush on a girl at school, Elaine - who’s kind of the bully/popular kid. The school principal is a well-rounded black woman. Guybrush’s dad needs a new car (hello Stan!), their house burns down in a series of events triggered by his brother Chuck (the insurance agent shows up, hello Stan!), …
And then maybe, just maybe, in the end you do return to the old Caribbean (travel agency: hello Stan!), somehow break the curse and be transported back to the MI1/MI2 universe.
Probably you would be disappointed when all of that would turn out to be just a Voodoo curse, because you enjoyed all the wonderful puzzles, dialogue and new characters you will miss (Guybrush’s dog, Spiffy!).