first contact dealt very heavily with post traumatic stress.
insurrection dealt heavily with .... insurrection.
generations dealt with the lamentations of being a has-been and dealt more with the difficulties of dealing with emotions.
nemesis dealt with the issues surrounding cloning.
by the way, you mentioned that he made an alternate time line, but actually he didn't. he tagged it onto the original timeline and essentially nullified it all with the events of that movie. check the link I posted, that article talks about that issue.
http://en.wikipedia.org/wiki/Star_Trek_%28film%29
They've been saying alternate timeline all along. Even Star Trek Online says it's an alternate timeline. The event of Romulus blowing up is true, but the Online game continues in the original timeline. Look at http://www.stowiki.org/Chronology for research. If I remember right, they had Picard become the ambassador to Vulcan, and Data became the captain of the Enterprise. I do remember that Geordi was the one who designed Spock's ship in the film.
And you make a point with those movies which are Next Generation flicks and its 4 vs 6. Not most by traditional standards but it felt like the word fit. I know the original series dealt with the issues before, but not as well as the next generation did. Yes I'm Picard all the way. The original six movies only dealt with societal issues once in The Undiscovered Country which talked about peace vs racial hate. Okay, so half and half then.
Insurrection really only talked about force relocation, not an insurrection against a whole government, and Nemesis didn't really talk about the issues of cloning. It talked about how someone personality is affected by their environment.
Well that is something we see with Star Trek: Into Darkness. The first film was at it's heart, an introduction to those who never seen the series. Remember parents who grew up with the original were bring kids to see it. The next flick will allow them to expand the new timeline, and flesh it out more since they have the introductions out of the way. Now I'm not saying it's the best film in the franchise, since that's between The Wrath of Khan, and First Contact, but it's sure a hellva lot better than The Motion Picture. Which badly ripped off some of 2001: A Space Odyssey's man vs machine elements, and semi copied random trippy visuals. Hell, The Voyage Home made a better and more enjoyable version of that flick.
As far as how he would treat The Guyver series, I think he would do a good job. Now the first guyver movie does have the protecting Mizky plot, but the film does completely wiped out the fact that Chronos is a world wide corporation. Even the FBI was trying to investigate them, while in the manga no one had a clue. Yes, the end of the film had the revelation that Max's(Mark Hamill's) boss as their agent but that didn't allude to the larger scale at all. It was sequel bait. The whole campyness erased a serious point the movie could've had, and the original version of Sean was almost as bad as Shinji from Neon Genesis Evangelion. Come on, Sho had backbone!
I believe J.J. Abrams would address all those points, and wouldn't just flood the story with jokes. I think you should still see Super 8. Yes it's his own flick, but it does show what he can do as a writer, and a director.
I will say this however. Those lens flares do need to go. They were both in Star Trek(pretty bad especially in the first scene), and Super 8(not as bad but still noticable). They can look cool as long as they aren't everywhere.
Additional:
As long as we don't get Uwe Boll. I will be happy.