Well, sorry, but if it's stated in the movie, you don't need to look anywhere else.
If Khan says that Marcus's mission is X, but what is demonstrated on screen doesn't support that and I ask "what is Marcus' plan?", do you still insist that it is X?
Name one thing that wouldn't have been accomplished without ANY of the characters, save Spock, Kirk, Scotty and Marcus ? You could literally have three people on the Enterprise and everything would have happened the same way.
I have to disagree. I haven't studied every significant role in the movie, but even when a character like Chekhov doesn't get particularly Chekhov-appropriate tasks to do, he still ran engineering and fixed the warp drive and saved Kirk and Scotty. Removing Chekhov from the movie would require someone else to be promoted to chief engineer. For Carol, literally everything she does would have been achieved without her character being there.
About Khan and item 16, you may be right. If I watched the movie again, maybe I would pick up a little more that Khan is biding his time and planning. I didn't get that the first watch. I did enjoy Cumberbatch's performance and I did think that he was the aggrieved party, which is why I thought for a moment he would convince Kirk to go after the worse bad guy. It worked that way a little bit, and in the end maybe Kirk's betrayal of Khan on the Vengeance's bridge destroyed any chance of Khan saving his men and accepting punishment, but overall Khan seemed to me to be so enraged that all that came through was a desire to destroy everything. I guess I just expected a little more depth to the character/plotting, and didn't feel like I got it. I wouldn't mind rewatching just Khan and seeing if there are elements I missed, I just wish I didn't have to work through all the rest of it to see it.
Of course other Star Trek episodes have demonstrated these issues but mostly individually or in small groups, and of course I have noticed them, but I think something of what I am trying to indicate here is how STID piles all of the nitpicks on top of the plot holes on top of the nonsensical plotting, on top of the poor characterizations, on top of the too-rapid pace, on top of ... everything else. If I have to dig through all of these things to find the supposedly "good" movie hiding underneath, I don't think there is much of a movie left that can be considered good.