Fundamentalist Trekkies....

[Cyberman]

This, as you know, is much more damning than the Enterprise making a whoosh sound as it speeds by in space.

That was a creative decision by Roddenberry (I think) to add a sense of dramatic realism, believe it or not. Obviously sound wouldn't carry in space, but audiences are so conditioned to expect the sound of a vehicle going past in everyday life that the lack of it tends to throw the viewer out of the scene. That's also why starships always appear fully or dramatically lighted even when in deep space and nowhere near a light source. Interestingly, the original concept for representing faster-than-light travel on screen was to have the Enterprise become invisible when at warp speed; though probably realistically accurate, it was deemed to look a bit silly. If I remember correctly, the original pilot episode shows how it would have looked.

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As for the whales, yes that is a ridiculous idea which probably would have stood rethinking. However, as Moros said, there is a basic format for Star Trek and even in The Voyage Home, that format was adhered to. Kirk et al behaved faithfully to their character, the technology worked as it was expected to, and so on. Star Fleet Headquarters didn't look like an old brewery because the director thought it'd be a nice idea, for instance; the new Enterprise at the end wasn't suddenly meant to be twice as big as it was designed, for another.