I think the simpler explanation is that TMP is just a lousy movie.
No, it's not. Sure it can be as simple as perception, but it actually accomplishes most of what it sets out to do.
The thing is a lot depends on what you expect from the film as opposed to what it's aiming for.
I'm reminded of a friend who said he didn't enjoy
Watchmen because it wasn't the kind of traditional superhero film he expected. But
Watchmen was never meant to be that kind of film particularly considering its source materiel. So it isn't the film's failing that it wasn't what my friend expected because it wasn't trying to be that kind of movie. My friend expected something
Watchmen was never going to deliver.
TMP was never meant to be a run-and-jump space adventure. And many of TOS' episodes, even some damn fine ones, were not run-and-jump adventures.
TWOK is more like a run-and-jump adventure, and it has some decent character moments because the characters are portrayed in a more familiar way. But at the core TWOK isn't as well thought or as credible (character wise) as TMP. THere is a lot of dumb thinking in TWOK.
But TWOK is like a lot of action films: if you have sufficient flash you can get away with a lot of nonsense.
I have said it before, but I don't think the really heavy criticism of TMP came around till '83 when TMP was shown on the ABC Sunday Night Movie.
No. It was immediate and widespread upon the film's initial release in 1979.
And yet the film made decent money and is one of the better performing films in the franchise.