Look, it didn't have to be Khan. Although if I remember right, Khan's tube started to thaw on its own in "Space Seed" (since he was the leader). So that probably happened when Khan was discovered in the new universe, too. Of course, Marcus could have thawed out someone called Timothy Wilberforce Lucas, the augmented ruler of the British Commonwealth in 1996, for all it mattered. The story could've been the same. (And it would've allowed a great line of its own. In the brig, instead of Cumberbatch ending his story by saying, "My name is, Khan." He could've said, "There are some who call me, Tim.")
The fun was it was Khan. That's all. And to the extent it did add some publicity, that didn't hurt. (I'm sorry, the secret that it wasn't Khan wasn't that secret -- Abrams and his people are better than that.) It creates some nice symmetry, too. It means that in both universes, Khan was the catalyst that allowed Kirk to turn himself around at a critical point in his life. In both universes, Kirk needed Khan.
So, Timothy Wilberforce Lucas, or Khan? It was basically one nice, big, blatant Easter Egg, even if not all fans could appreciate it.