I find it interesting that, as of January 18, 1982, the
second film was being called 'The Undiscovered Country' (or, alternately, Star Trek: The Motion Picture II), even though it was the same Khan story that we know:
If Nimoy had not participated at all, there was still plenty of room for a good story that could have retained a lot of the same elements.
The Genesis project could have been at the heart of a conspiracy such as we saw in the sixth film. All that business about Kirk being kept out of the loop about the ongoing Genesis planet story seemed a little odd, to begin with. He was still a full admiral and he had been right in the middle of the events.
"Only the science team goes to Genesis." Horse hockey. One little Oberth-class science vessel to deal with something so unprecedented?!?
Kirk would have been highly suspicious of that. He would have stolen the Enterprise just to go make sure that his son was safe!
While TSFS is my favorite of the films,
much could have been done better.
Same with TWOK. Kirk would not have gotten caught with his pants down. That was wildly out-of-character.