It would be epic if the Dark Apprentice were the real Starkiller (That would mean that we were playing with a clone this whole time, but the campaign was bad enough anyway).
After all, he did say, "I wonder if he is here."
If Vader is using the cloning story as a way to make the real Marek obedient, the Dark Apprentice would be just as likely a target as Starkiller.
There really is no evidence for this, but that's what makes it so intriguing.
Maybe the Dark Apprentice was the only subject strong enough to resist his feelings because he isn't a clone.
Maybe the "birth" scene depicts the real Marek waking up from a regenerative coma.
Maybe I've left the galaxy on this one.