I'm not putting this in spoiler code since it's just speculation and the thread title says "Spoiler" twice anyway. Just don't read on if for some odd reason you're in this thread despite trying to avoid spoilers.
My suspicion that Cumberbatch might be Khan has hinged not only on the several allusions to TWoK
in this film, but also to a couple of the original names for Khan in the early drafts of Space Seed
In writer Carey Wilber's original treatment, the Khan character is a Nordic superman named Harold Erricsen. This evolved in the first draft, where the character first introduces himself as John Ericssen, but is later revealed to be Ragnar Thorwald, who was involved in "the First World Tyranny". (Star Trek Magazine issue 120, The Star Trek Compendium, pp. 57-58)
becomes John Harrison. Also, he initially gives a false identity to conceal his infamous name, just as it's been speculated Harrison might be doing here.
Given Orci and Kurtzman's (especially Orci's) knowledge and referencing of Trek lore, and the fact that they would undoubtedly have researched Space Seed
extensively while working on the script, that seems like something they might do to give the villain a name that's a hint but at the same time deniable and not completely obvious.
Also, we have the issue of Harrison's seemingly superhuman jumping and massive weapon wielding ability on the Klingon planet, his assertion that he has the ability to cure fatal diseases beyond the abilities of Federation medicine, and while a quest for vengeance is hardly unique to Khan, it's kind of the thing he's known for.
If I had to take a stab at a potential plot, I'd guess that due to Starfleet's enhanced technology and different priorities in the wake of the attack on the USS Kelvin 25 years in the past, the then Captain Marcus or someone else discovered the SS Botany Bay much earlier than it was found in the Prime Timeline, and after an attempt at seizing his ship, Khan and his followers were banished to Ceti Alpha V like before.
In this timeline, years later, Ceti Alpha VI was used by Carol Marcus as a test site for her proto-Genesis torpedo, and like in STIII
, it failed and wound up destroying the planet. "The shock shifted the orbit of Ceti Alpha V and everything was laid wasted." This may be the desolate planet with the huge rock formations that Harrison is shown staring at in the trailer. Harrison is able to save many of his fellow Augments by having them go back into their cryogenics stasis pods again where they don't need food or water the planet can no longer provide while he goes off on his mission.
Now Admiral Marcus and the top brass consider it a blessing in disguise that Khan and his dangerous band of Augments probably have been killed off and neglect to send a rescue mission after them. This is what prompts Harrison to say that Starfleet's leaders have committed a terrible crime and to seek vengeance by going undercover and infiltrating Starfleet to destroy their facilities, attack their leadership, gain access to a ship(s), and possibly grab the new and improved Genesis Device, which like many horrible things is being developed with the best of intentions in order to terraform (vulcaform?) a new homeworld for the Vulcan refugees similar to Vulcan itself.