Spoilers: The "bad guy" wasnt really who he said he was!

[BillJ]

What possible motive would S31 have for over-riding the pre-programmed sequence?

To do some research? Kirk and Company knew they had the SS Botany Bay before ever going over. Section 31 would've likely did all the investigative work about the ship before beaming over and dug deep to learn everything they could about the passengers and ship, including how the control the cryogenic process.

I think that the intention of the writers is that Cumberbatch is Khan. But I think they intentionally left themselves some wiggle room.

 

[Pavonis]

Perhaps they had motive to override the automatic awakening of Khan, but would they have the ability? The Botany Bay and her cryotube crew were so antiquated that McCoy and Marcus couldn't figure the systems out immediately. Would the S31 personnel know more than anyone else about Khan's era and its technology?

Kirk and his crew just stumbled over Khan and his crew. This time, Marcus and S31 may have set out to find the Botany Bay, but the records from that era would not have been anymore complete than in the original timeline. And if S31 wanted the best mind of the Augments, their best leader, why would they pick a tube at random? If they wanted Khan, they'd figure out which one was Khan and wake him. If they didn't care which one they woke up, why would they override the pre-programmed sequence (which would give them Khan anyway)?

 

[Ovation]

One--Being Sikh is a religion, not an ethnicity.
Two--There are pale skinned people, even today, in the region of the former British colony of India.
Three--Genetic engineering most likely guarantees an ethnic mix without any guarantee of which traits are dominant.
Four--Different actor.

Et c'est tout.

 

[Agent Richard07]

They did try to get Benicio Del Toro first, Cumberbatch wasn't their first choice.

When the 2009 movie came out, the writers mentioned Javier Bardem as their ideal choice. He would have been good. I wonder if he was ever asked.

Also, Khan and his people weren't in cryotubes when they were found in the Botany Bay in TOS, so why are they in them in this movie? Anyone have a good in-story explanation for that?

 

[Oso Blanco]

According to Bob Orci, the After Darkness comics will explain why this Khan wa so different. See the thread about Kirk's blue eyes.

 

[JackSparrowJive]

In "Space Seed", the first hibernation chamber to activate was Khan's, and it was a per-programmed action when the ship's systems were powered up by Scotty.

In the new timeline, presumably the same sequence of events would unfold. Khan's cryotube would be the first activated when the ship was found by Section 31. What possible motive would S31 have for over-riding the pre-programmed sequence?

This could be easily explained with a little imagination. Remember, Marcus/Section 31 was actually looking for Khan in this timeline; so when they found the Botany Bay, they knew they had found him. My point? Why would they even bother powering up the ship like Scotty did? Maybe they just took all the cryo-tubes off the ship and blew it up. Then they could have woke them up later in their own secure facility. And without being hooked up to the ship, the pre-programmed sequence of Khan's tube waking up first wouldnt have happened.

 

[Belz...]

We don't know if they really knew who they had just found when they found the Botany Bay.

 

[Greg Cox]

Yes, clearly they should have gone with an authentically Indian actor like . . . Benecio Del Toro? Javier Bardem?

 

[spinnerlys]

Yes, clearly they should have gone with an authentically Indian actor like . . . Benecio Del Toro? Javier Bardem?

Or even Ricardo Gonzalo Pedro Montalbán Merino for that matter.

 

[Oso Blanco]

Marcus/Section 31 was actually looking for Khan in this timeline

I don't they were specifically looking for Khan and the Botany Bay. How would they even know about them? Spock Prime clearly didn't tell them. I think they found them accidentially, it's just that they were exploring space faster and more aggressively.

 

[OpenMaw]

The way Marcus said those things implies to me that what they were doing is intense intelligence gathering. Anything they could find to give them an edge. Khan was not the end goal, he was just a lucky goldmine.

 

[CorporalClegg]

I don't see it.