I've been mulling it over and trying to understand a bit more why I felt so disappointed with STID and I've come to realise how one-sided its approach was to the only topic of social commentary it addressed; the war on terror. It's this whole war on terror topic which gives STID its apparent depth, insight and food for thought. If anything STID comes over as almost a subtle endorsement of the war on terror.
It comes down to the consequences (or lack of you) you see. After everything that happened in Qo'noS I'm surprised the Klingons didn't just declare war on the Federation. They would have all the reasons: a Starfleet ship trespasses in their territory, Klingon warriors/soldiers killed and so forth. They could have slipped in a scene about how a war nearly started or even a war has happened and that incident in Qo'noS played a large part in starting it. It would have been a very nice wrap-up to the consequences and magnitude of what happened, but STID tossed this aside.
Little or large, it is an omission, and omission which implies that it's okay to violate a state or nation's territory to catch the bad guys. I mean for a man of principles, it really bugs me that Kirk was so gungho about the mission to capture/eliminate Khan in the first place. It's all about shear gut instinct and it is hard to address principles when they are so detached from logic or reason. For instance you have Spock who wants to follow by the book, and yet he goes along with this dubious mission. Of course all of that is eclipsed by Spock beating up Khan.
STID is all about emotion, that takes precedent over everything else. Logic, plausibility, continuity and motives be damned! That's why things feel so forced and clumsy, it's why Kirk had to weep when Pike died as if Pike was some sort of family figure, why Spock had to go utterly ballistic and why Khan had to crash the Vengeance into San Francisco because... ? It's like the film is trying to beat you into submission with non-stop action, breakneck pace and heart-throbbing emotion. STID worked best in these scenes where it became analytical and was presenting a situation (without force-feeding it down the viewer's throat): Khan revealing his identity to Kirk, Admiral Marcus warmongering aims, Kirk and Pike in the bar, and of course Spock talking about why he maintains this emotional distance. The last scene was the only scene where I was rather moved, it was dignified if you know what I mean. I wish STID had more moments like that I really do, indeed it was probably the only actual bit of character development in the film that did not feel absurd.