I had the same reaction when I watched the film again about a year ago. This film is BAD! Not bad by Star Trek standards bad, but bad by Filipino action movie standards! I always remembered 3 as the worst of the bunch, but I can't possibly believe it could be worse than this film. Some things that bothered me:
Why does a race as advanced as the Vulcans choose not to have their babies in modern, clean, sterile hospitals, but on stone slabs, outdoors in the middle of nowhere?
How does a man as smart as Sarek not realize that there is something called genetics that influences your children? If you knock up a human, chances are your kid will be half human. Why does Sarek choose to knock up a human if he doesn't want a baby with any human in it? What is it about a newborn baby that isn't Vulcan enough for Sarek? Why does Sarek keep marrying these human bitches if he doesn't like humans?
Everyone has a secret pain. Really? In the 23rd century with all the evolving humans have done every single one of them is still carrying around a hidden pain? And just one hidden pain? And all you have to do is re-live that pain and you have no more pain? But in exchange it does make you a mindless zombie who blindly follows a madman? It doesn't actually seem like getting rid of your pain is a good thing.
So what is actually so special about Sha Ka Ree and the dude that lives there that Sybok is sure that this the home of God? Is the being in contact with Sybok? So he can communicate with someone half way across the galaxy, but he can't get off the planet without a ship? Isn't much of a "God" either if he can be taken out with one shot.
I am not sure I can picture a Commander in Afghanistan looking at an al-Qaeda base wondering how to best attack and thinking "I know, a distraction. I'll get one of the chicks from the engineering corp to get naked and writhe around. She won't mind."
Even in a warrior culture like the Klingons are individual ship captains really allowed to attack anybody they want even if it mean inter-galactic war?