The theory in the newsarama article makes a lot of sense. Even if it isn't completely right, I believe it's closer to the truth than all the other theories.
I can even imagine what the reveal will be:
John Harrison: No, Kirk....Khan is my great..great... grandfather!!!
Captain Kirk: Nooooooo!!!!
:"Kirk, you can destroy the Emperor, he has forseen this. It is your destiny, join me and together we will rule the galaxy..."
oh wait, wrong franchises.
Well, there is this quote from Khan in "Space Seed", although he's directing it to Mr. Scott and not Kirk: "Improve a mechanical device and you may double productivity. But improve man and you gain a thousand fold. I am such a man. Join me. I'll treat you well. I need your training to operate a vessel this complex."
In other words, "Give yourself to the dark side, Scotty."