You know as much as I disliked this film I can easily see where a lot of things could have been fixed to get a better film. One of the biggest fixes would have been to have a genuinely interesting villian, someone that actually wasn't just a baddy yet someone with nuance that you could possibly even sympathize with.
One of the strengths of TWOK is that Khan wasn't just a cliche bad guy. You could actually see his point of view. Nero doesn't really come off that way despite the words he says.
Look I still think
Star Trek II: The Wrath of Khan was the best Star trek film made to date, bar none; but it too has major major plot and science holes you could fly a Starship through:
1) Chekov aboard the U.S. S. Reliant MISTAKES Ceti Alpha V for ceti Alpha VI; and couldn't tell that there was a planet missing from the star system; NOR see the debis that must have been left from the explosion?
2) The Relient's sensor show the planet as unable to support life (and they're only going down to check if the planet MIGHT have a microbe on it; and even been down in full spacesuits - Yet Khan and his people have been living for near 15 years by putting a veil over their mouths and have somehow managed to obtain enough food and water from the destroyed ecosphere. (What? Were the Reliant's senors in that much need of an overhaul; or were Chekov and crew THAT incompotent as to not be able to use/read the senors properly?).
3) In
Space Seed all of the survivors in Khan's group were in their early 20ies or 30ies and not all 'Blonde' - YET, 15 years later - the majority look to STILL be twentry-something; and 'Yachim' (who acts like Khan's son; but is older that 15 years); yet, by Khan's OWN words, Lt. Marla McGivers (his wife) was killed by one of the brain slug birthing creatures soon after they arrived - PLUS Ceti Alpha VI exploded 6 months after they were left there. Given all this, do you think any women of Khan's group would have the tim or inclination to get pregnant; or further that with resources so scarce, Kahn would allow an infant to survive at the cost of the colony?).
4) Khan wants Kirk DEAD; yet as he chases Kirk into the Nebula, he only fires ONE tordepo as a 'warning shot' - which Kirk interprets as such when he says "They just don't want us going in there." Also later, we do see that the Reliant does still hav working phasers. My point? If Khan is so vengeful at that point; and is in weapons range (which is shown by his firing of the torpedo); WHY IN HELL wouldn't he let loose a full fire barage as he was chasing the 1701 toward the Nebula. Ye, some real 'superior intellect' displayed there, eh?
But even with all the above; my overall enjoyment of the story and characters as presented in it is not detracted from.
My point, if you really look at the majority of any popular films; you can find stuff to pick apart ad nausem.
The new Star Trek does have a number of plot holes and contrivences done specifically to more the story along and keep it interesting, much like STII:TWoK did; yet it still doesn't detract from my enjoyment of what was untimately a good and entertaining Star Trek film with good characters, and better acting and direction then we've seen in a looong time.