I actually agree with you on all these points. I really am having a hard time pointing out what bugged me about this film as compared to ST09, which I loved. Its like something was missing, but I can't put my finger on it. Maybe my second viewing will enlighten me.
I think it might have been stronger if they had dug a bit more in Marcus' plan and Khan's backstory. But doing either of those things would've simply opened them up to more criticism if it didn't exactly match what some people had in their heads.
So that is kind of a "damned if they do, damned if they don't" scenario.