I certainly agree that John Harrison was more interesting than Khan, and even made a thread to that effect
. And certainly since Orci has described the creative process for the character as creating and developing a new character who he then named Khan kind of makes it really pointless for the character to be Khan.
Just what is accomplished by this anyway? It's not marketing, they kept the Khan identity top secret thereby preventing them from taking advantage of any marketing opportunity this idea presents itself with.
One could argue dramatic effect. It would be completely out of left field for Harrison, sitting in the brig to announce he's Khan. And I suppose it would have been if the Abrams posse hadn't constantly been saying there's a twist to the Harrison character related to Trek canon like snickering school children telling the loser kid they know who has a crush on him but refusing to reveal who exactly.
I get the impression they are in love with plot twists and wanted to try their hand at a twist which will be forever remembered in movie history like Vader revealing he's Luke's father. Instead they completely ruined it just made themselves look like petulant children and by extension unprofessional filmmakers.
Or, they like "TWOK is our favourite movie and we really wanted to revisit it. So we remade its most memorable scene and named our villain Khan."
A better approach would have been to stick to the John Harrison character as the villain or if they wanted to use Khan so badly been upfront about it, actually write and develop the character as Khan, and announced to the world as soon as Cumberbatch was cast that he was indeed Khan.