I think everyone can agree that Wrath of Khan was where pretty much all the ingredients went together as good as they could, and gave us the blueprint for what a Star Trek film could be.
As to Into Darkness.. I thought Benedict played the character that was written well, I'm just not sure I'd agree it was a well-written Khan. You had the cold, calculating intellect and ruthlessness, but none of the charm and joviality. Where was the figure that could inspire loyalty unto death from his followers and could tempt his enemies into becoming his allies and turn on their friends?