Here are my couple of gripes with Into Darkness. I loved the story actually but my only problem with using Khan was that the audience knows he is a big threat only because of other episode/movie that have nothing to do with this movie. To this crew and time-line Khan had not earned that reputation yet. So to me the threat of Khan didn't feel authentic. I think the entire death and re-birth of Kirk was forced and really didn't have the emotional bang Spock's death had in TWOK. We hardly knew this Kirk. All in all through I did like the movie a lot.
I agree, in part. I really don't think Harrison needed to be Khan. Marcus was plenty of villain for the film, and Harrison would be fine as Harrison, serving as the genetically engineered weapon who went wrong.
However, Kirk's death was still one of my favorite scenes in the whole of the two films. It worked so well for me.