Even as an else-worlds "What would Kirk and Spock do if they had traded places?" is the answer to that question really "Spock would act just like William Shatner?" Also they did such a poor job establishing Kahn that they literally had to have Old Spock show up and explain to the characters and to the audience why they should even care who he is. The film has pretty much zero consequences or stakes, killing off a character and bringing him back 5 minutes later. True they brought Spock back to life in the old films, not that that was the best idea to begin with, but even then it took major sacrifices to do so. Its less a matter of being hung up as a fan and more to do with the fact that the film had absolutely dreadful story telling, relying upon appropriating beats from an iconic film to draw out an emotional response. There are similar problems in Super 8, a movie I actually enjoy very much, but it tries its damnedest to have an E.T. ending without having the kind of story to back that up. Its unearned and unsupported. JJ is good at getting at the texture of things but fumbles the content.
I still think STID's story works enough. Yes I don't deny the hodgepodge of all the stories together, and the explanation etc, but it still works as an entertaining adventure. To me still better then a lot of most the TNG films, and V/III. But I think the story telling still worked enough. Even with "picky" critics, the films still was received well. I think the characterization still worked enough to pull the film through. And I think giving Spock the reversal actually worked to see that half human side. And cement a relationship between the two.
I agree that Super 8 the third act with the Alien, he fumbled with that. Really Super 8 was a film that was about kids and coming to age by making a film together. Later the "alien" story was put in. Which the first 2 acts did great with, but the alien story in the third act fizzled. As with you I enjoy the film a lot.
However ST09 was brilliant. Ya it was Trek light but as a story it earned everything in it. And I think STID was more of the script problem then anything else. Which is why I fear for the third one because of Robert circling around the director's chair.
But I think with each film JJ seems to learn. He admitted the faults with STID, and poked fun at himself with lens flare etc.
But when it comes to SW, I think he is the one to have. I think it's one thing he is extremely passionate about. I think (which is rare) dark b is right on that. JJ unlike Trek cares about SW, and I know will do great with it. I think it's one thing he truly gets.
As for Nolan, the more I think about it, I don't know if he could do a SW film. I think a film like CEOT3K he could. Which this seems to be pulling from.