Don't shoot me. I am not here to bash trek. I enjoy the heck out of Trek, but STID, while it had the potential to be great, was just bad. A lot of that was lack of self identity and horrid writing, seriously bad writing. So bad that I had to list nine scenes minimum to fix the story.
This movie could have been great. It should not have been a retelling of TWOK but of Space Seed. Imagine changing just these scenes and how it would have changed, and maybe improved the film:
1: Opening, Kirk and McCoy distract the aliens so that the Big-E can blast open the caldera of the volcano from the opposite side, or beneath the water, venting the volcano harmlessly. The shuttle must provide targeting data however and crashes due to proximity to the volcano, mandating the Big-E to go atmospheric and reveal itself to save Spock. You have inherently the same scene with Spock; waiting for the inevitable before Kirk rushes in to the rescue without the need for the silly underwater scenes (sorry spaceships aren't built to go underwater, Scotty even comments on that).
2: Kirk does not lose his command due to the potential political fallout. Instead Admiral Pike will transfer his flag to the Enterprise in order to keep Kirk on a tighter leash. Remember, Kirk and crew saved the Earth in the last movie, to send him back to the academy would make the public question Starfleet in a huge way. If instead, they just see an Admiral actually command the fleet's flagship, they will accept that much more readily.
3: The transwarp pod (the biggest Pandora's box in the movie) doesn't send Kahn to Kronos, but to a freighter passing by the Sol system. Kirk and crew then rush off after it instead after seeing that its course has changed towards Klingon Terrritory. Scotty also remarks that the pod burned itself out upon usage (just like the one that beemed him and Kirk to the Big-E in the last film).
4: The Kirk/Scotty argument proceeds much the same, but Kirk begins to see the cracks in what is going on, and instead of firing Scotty, subtly sends him to investigate.
5: Added scene, Kirk and Crew catch up to the freighter, after several days and the captain (Mudd?) reveals that Kahn commandeered a shuttle to escape to Kronos. The timeframe issue in this movie was just bad, no Trek movie, series, or book has ever said that Earth and Kronos were within a day of each other. Several movies of late have done this, either having a nebulously short time line (SW-VII), or making everything seem to take place in an absurdly short amount of time (Ghostbusters 2016).
6. Make mention that the abandoned area of Kronos where they find Kahn is that way due to Nuclear Fallout. This will come into play later, and explain some of McCoy's motivations to study Kahn's blood.
"He spent enough time in that irradiated waste land to kill you three times already, Jim. He has an unusual resistance to radiation."
7: Scotty takes the coordinates Kahn provides and uses a repaired Transwarp pod to beam to the top secret facility without his little buddy. Remember, this is a top secret facility, and he just flies on in with the rest of the crew with no identification and no question asked. Also, a little easter egg could be thrown in here and after Scotty beams aboard the Vengeance, Porthos materializes after years of being trapped in a matter stream from Scotty's experiment he mentioned in the last film.
8: While the Enterprise is falling towards Earth, again after taking several days to get back, Spock informs Kahn that they have his crew alive but unless they save the Enterprise his crew will die. Kahn teleports direct to engineering and prevents Kirk from entering the warp core. He then saves the Enterprise, forcing a debt upon Kirk and asks Kirk to take his crew someplace safe, where they and the Federation won't come into contact. But he also asks that he send his body with them, so that they can mourn properly.
Kirk and Spock can still have a scene, not as touching, where Spock comments how Kirk was about to sacrifice himself to save the ship. Also have McCoy pronounce Kahn dead, but put back into a stasis pod.
9: Instead of the Vengeance crashing, the restored Big-E, and other ships, able to get out of Space Dock in an emergency, grab the ship before it can crash, saving millions of lives. This was another major plot hole, where did all those other ships in space dock go? I get that the captains of several ships were killed by Kahn earlier, but none of those ships had crews that could fly them?
10: Kirk implores the Federation to allow him to deliver Kahn's body, and the rest of his crew, to an out of the way, in hospitable world they discovered (Ceti-Alpha Six) where they will live without technology in the hopes that they will eventually develop a more peaceful society. This leads into McCoy complaining that he wanted to study Kahn longer, and his remarkable resistance to radiation, and a post credits scene where we see Kahn's colony some time later (years preferably). We see a man plowing a field, he looks up and smiles, revealing that Kahn is still alive.
Ok, so that went long and was ten scenes. There would be some other small, subtle changes as a result of these, but that would, IMHO, take care of many of the issues people had with the film, and create an ability to have a true NuTrek TWOK later on down the line, or allow a possible remerge of the timelines.
Also, STID created several big Pandora's Boxes: The Transwarp Pod (makes ships all but obsolete), Kahn's super blood (renders people immune to death), Super Fast Warp Drive (can cross distance to major adversary's planet and back in two days), Super Torpedoes (Can be fired distances of light years away). These changes close the lids on those boxes and mitigates the issues they created. Is it perfect, no, is it better, I think so.
Will I do one of these for ST: Beyond? I don't think so. I thoroughly enjoyed that movie, and while there were some plot holes, none of them were movie breaking. It was a fun movie. As for my next movie to go after, I am open to suggestions.