Before we get in to the nuts and bolts of Star Trek Into Darkness, let us take a moment to see what the studio behind the film wants us to believe the movie is about:
When the crew of the Enterprise is called back home, they find an unstoppable force of terror from within their own organization has detonated the fleet and everything it stands for, leaving our world in a state of crisis. With a personal score to settle, Captain Kirk leads a manhunt to a war-zone world to capture a one man weapon of mass destruction.
Now, because this is a J.J. Abrams flick, we all knew that we were going to have to take this synopsis with a grain of salt. At least it gave fans something to spend the run up to the movie debating about: who is this "one man weapon of mass destruction?"
The answer ended up being Khan, but the reality of the situation was that the answer was always going to be Khan. Oh sure, it might be fun to speculate that the villain of Into Darkness was going to be someone else, but now that Star Trek has gone mainstream the only way to truly take things up a notch in the sequel was to make the bad guy the biggest bad guy around.
That begs the question: why go through the trouble of keeping a character like Khan a secret? Why not put that fact out front and center in the official synopsis, the trailers, and the rest of the marketing campaign? It seems like a lot of people would be really jazzed to see the rebooted Trek characters taking on the original Trek's greatest enemy.
There are two schools of thought here:
1. The "J.J. Abrams Loves A Good Mystery" Theory
Everyone knows that Abrams has a thing about mysteries. Lost was about an island with more mysteries than the detective fiction section of your local library. Mystery made up the entire advertising campaign behind the Abrams produced Cloverfield. Mystery was the subject of his Ted Talk.
It is entirely possible that Abrams and company thought the film needed a serious "Holy shit!" moment, one provided by the revelation that the heroes were not just going up against a terrorist, but that they were going up against the most dangerous man in the galaxy.
2. The "How Can We Avoid Whitewashing Accusations?" Theory
In the original Star Trek Khan was played by Mexican actor Ricardo Montalbán. In Into Darkness he's played by British actor Benedict Cumberbatch. The character, as discussed in the original series, is supposed to be of North Indian ancestry. There's a very interesting discussion to be had about the casting of Khan that's been largely swept under the rug (but not completely) because no one wants to be the jerk who spoils the movie.
Could hiding the true identity of the character Cumberbatch plays be a way to avoid the negative talk and cries of whitewashing (having white actors play non-white characters)? Perhaps, but that requires one to hold some very cynical opinions on the situation.