I don’t know if it would qualify as a “minor” change, but I think the best thing they could have done to improve the story would be to clarify Nero’s rather muddled motivations. Seemingly, his number one goal in life after the destruction of Romulus was to avenge himself on Spock, the one person who actually tried to save his planet. After that, he planned to destroy the entire Federation, even though the Federation had nothing to do with what happened to Romulus. It was hinted at in the Countdown comics that Nero believed Spock and the Federation deliberately allowed the Hobus supernova to destroy Romulus before intervening to stop it, but this is never really explained in the movie. We’re left to conclude that Nero is simply mad with grief and determined to make the rest of galaxy suffer along with him, which works pretty well up to a point but still leaves a lot of questions unanswered.
Another quandary is why, after finding themselves more than a century in the past, Nero and his crew didn’t fly straight back to Romulus to deliver the Narada and its advanced technology to the Empire instead of pursuing a reckless quest for revenge. Yeah, I know, they got captured by the Klingons and imprisoned for 25 years, but they eventually escaped, recovered the Narada and had the same decision to make. Again, the Countdown comic reveals that Nero was equally as pissed off at his own government as he was with Spock and the Federation for ignoring the Hobus threat and refusing to even evacuate Romulus until it was too late. If Ayel and enough of the rest of his crew felt the same way, it’s a lot more plausible that he wouldn’t run straight home to Mother Romulus. His conversation with Captain Pike made it clear that Nero wanted to bring about a very different Romulan Empire, one that was free of the Federation’s constraints, and he may have felt the best way to do that was to take matters into his own hands rather than trust in the government that had already failed him. Again, though, this was only vaguely alluded to in the actual movie.
I thought the mind meld between Kirk and Spock Prime as an expositional method of delivering the film’s back story was rather clunky. I would have preferred that they had given us some extra scenes with Nero and his crew to fill in most of those details, as well as giving us a clearer picture of who they were and why they were doing what they were doing. They could have spread these extra and expanded scenes out throughout the movie so that all the pieces of the puzzle came together at about the same point, when Spock Prime was first revealed.
There are other things that might have helped as well. I think it would have given the plot a big plausibility boost if Kirk had been a bit further along in his career when the crisis developed. There’s no particular reason he had to have taken the Kobayashi Maru test as a cadet, he could have already been a commissioned officer with some ship-board experience under his belt, back at the Academy to take the test as part of his advanced command training. He still could have been placed on suspension and denied an emergency ship assignment, with almost everything else playing out just as it did in the movie, except a lot more believably. I would actually love to see this issue addressed in the sequel, with Kirk getting some grief for attaining command without “paying his dues.” Maybe even the revelation that his promotion was pushed through as a political maneuver over the objections of the Starfleet brass; the frightened Federation public, still wounded from the loss of Vulcan, demanded their hero and the Federation council obliged. As a major subplot, Kirk may find keeping command of the Enterpriseis every bit as difficult as achieving it in the first place.
I also wasn’t keen on the whole business of Spock ejecting Kirk in an escape pod onto so-called Delta Vega. One could argue that Spock was, indeed, emotionally compromised and just made a bad decision out of spite, but it still seemed like a contrivance with no purpose other than to allow Kirk to meet Spock Prime and bring Scotty back aboard the Enterprise. I’m not sure how they would have accomplished those things otherwise, at least not without some pretty significant plot revisions, but I’m sure it could have been done.
There are probably a dozen other minor things that could have made it a better movie, IMHO, but those are the main things I had a problem with and most everything else is just nitpicking.
