It does make me wonder though by the time they got around to TVH, did they say, "hey Gene, we love the time travel idea. But hey, instead of your JFK angle, how about we go back and get some whales instead?"
That's actually a reasonable approximation of what happened. With each film, Roddenberry spent more and more time typing up angry, hateful memos that he circulated around the Paramount lot for everyone to read. Harve Bennett finally realized that the only way to get him to stop was to try to praise as many of his script ideas as possible in order to make him feel like the films were still his creation while still keeping the major story elements in line with what Bennett and Nimoy wanted. So when Roddenberry pitched his JFK idea again, Bennett and Nick Meyer told him they liked the time travel idea but that they wanted to use it differently.
TVH is actually a combination of two scripts put together. Bennett wrote the film's beginning and end. Meyer has everything in the middle, including the bulk of the San Francisco scenes, as he used a lot of ideas that were in Time After Time