In the lead-up to Star Trek Into Darkness, co-writer Damon Lindelof said that the reason for the secrecy was "the audience needs to have the same experience that the crew is having. You’re Kirk, you’re Spock, you’re McCoy, so if they don’t know who the bad guy is going to be in the movie, then you shouldn’t know."  Lindelof added that if people knew who the villain was before the movie opened, then it would have been a let-down when it was revealed in the movie.  Now that audiences have seen Star Trek Into Darkness, and opened the "mystery box", there's some curiosity about the spoilers that were so closely guarded throughout the film's production and marketing campaign.

Hit the jump for what Lindelof had to say about the villain and more [obviously, there are spoilers ahead for people who haven't seen Star Trek Into Darkness].

Speaking to MTV's Josh Horowitz, Lindelof explained that even though there was some discussion about whether or not to put Khan in the movie, it was pretty much a foregone conclusion.  Also, the character monologues in Wrath of Khan and therefore had to monologue in Into Darkness because monologing is cool when you have Benedict Cumberbatch do it:

As for our friend Mr. Harrison (I am still uncomfortable even typing his true identity, so conditioned I have become to not do so), yes — there was a fair amount of back and forth as to whether to take on such an iconic character. But it was never really a "Should we or shouldn't we?" as much as it was "We really have to do this but if we don't get it right people are going to kill us."

I think that character is so iconic — he has such an intense gravity in the Trek universe, we likely would have expended more energy NOT putting him in this movie than the other way around. But more importantly, Josh?

He monologues. He monologues like no one else. Pop in the original Star Trek II and watch the scene where poor Chekov stumbles into the Botany Bay. Seriously. In this day and age, most bad guys just run and jump and do that cool neck-breaking move and get the hell on with it. Outside of a Bond movie, does ANYONE monologue like this guy?

No, Josh. They do not.

And when you can get that monologue to come out of Benedict Cumberbatch's mouth, does the "writing" even matter? I mean, seriously, I made that guy say "Milk, milk lemonade, and this is where the fudge is made" and it scared the living sh*t out of me.

Lindelof also addressed making sure the film was an homage rather than a rip-off (I believe he and co-writers Roberto Orci and Alex Kurtzman failed horrendously in this regard) and why they chose to bring Kirk back after twenty minutes of death:

We were ever wary of the line between "reimagined homage" and "direct ripoff" and erred on the side of the former. As a fun FYI, Bob, Alex and I code-named the script file "PLANT STUDY" as we sent it back and forth.

We never considered leaving Kirk dead at the end of this movie. No one would've believed we'd leave him that way and in this spoiler-centric culture, the inter webs would have known we were bringing him back and how long before the release of STAR TREK KIRK IS BACK WE PROMISE.

I'm purposely avoiding talking about the blood thing, but by writing a sentence in response about it, it will feel like I'm not avoiding it completely.

Okay, it has nothing to do with "spoiler-centric culture".  It has to do with screenwriters being so scared to even attempt doing something original that there's no way they would have the balls to actually kill off Kirk for good, and you may as well get his resurrection over with before ripping off (I'm sorry, "making a 'reimagined homage'" of) The Search for Spock.

As for why they chose to bring in Spock Prime (Leonard Nimoy) to explain Khan to the crew of the Enterprise, Lindelof says:

It would have been hubris for us to represent to the uninitiated that Khan was our idea and there was no one better to pop in briefly and say — "Hey, these guys are just doing their own spin on a bad guy that was around a long time before they came along." The minute we stop honoring, acknowledging and representing the original Trek, we are bound to lose sight of the enormous gift we have been given in sustaining it.

It's fascinating to see that this is what Lindelof believes.  He truly thinks Into Darkness is a honor to the original Trek simply because they had to lazily explain something, and they got Nimoy to do it.  What an honor.

As for less controversial changes, Lindelof says that hundreds of titles were considered including "Star Trek: Vengeance", but that one was scrapped due to its similarity to Ghost Rider: Spirit of Vengeance.

Even though Admiral Marcus (Peter Weller) doesn't have a British accent, his daughter Carol (Alice Eve) does because she grew up in London, but a scene explaining this was cut (I had a lot of problems with the film, but this wasn't one of them).

And speaking of Alice Eve stripping down to her underwear and why that was necessary, I'll let Mr. Lindelof have the last word:

Why is Alice Eve in her underwear, gratuitously and unnecessarily, without any real effort made as to why in God's name she would undress in that circumstance? Well there's a very good answer for that. But I'm not telling you what it is. Because... uh... MYSTERY?