I did say it was a soft remake
. But I think you make a good point. I don't think Into Darkness is a total remake of TWOK but it does take some lines verbatim from the film-perhaps as an homage-and it does its own version of the engineering chamber death scene-as well as the infamous Khan yell. I felt all of those things felt like pale imitations that were largely unearned. To be fair, where Khan is concerned I think Into Darkness uses both Space Seed and TWOK.
It seems to me that ID Khan is a mixture of the two. As for TWOK I think Khan as a vengeance fueled maniac works just fine. I saw TWOK years before I saw Space Seed. It works even better for me after I saw Space Seed and saw more fully Khan's character arc, of how this smart, charismatic guy had descended into an embittered, hollowed out vengeful shell of himself.
But not taking Space Seed into account, TWOK Khan was a compelling villain who also used his intelligence and showed just a hint of his super strength. His fanaticism made him formidable and terrifying. He actually beat Kirk when he left him on the Genesis station, but his ego and his need for revenge blinded him. Similar flaws also plagued ID Khan. ID Khan did show more concern for his crew but TWOK Khan did lament his wife as well as the fallen condition of his people and that helped fuel his desire for vengeance similar to how the belief that his crew had been murdered by Spock drove ID Khan to make a suicide run at San Francisco/Starfleet HQ.
I didn't mind Kirk and Khan not meeting in TWOK. It actually made the movie stand out and it seems quaint now in this age of mega confrontations and beat downs. I think the structure of TWOK made the characters focus more on their wits and made the final starship battle tense and exciting in a way that Kirk facing down against Kruge or Soran were not. Not having the two face off was also a good thing for Kirk because as we saw in ID and in the Enterprise Augment arc an aging Kirk probably wouldn't have stood much of a chance against a Khan hellbent on killing him.
Keeping it on starships made it more of an equal footing for Kirk and it forced the writers to not rely on Khan's brute strength or some inexplicable reason for that failing (like it did in Space Seed) for Kirk to get the win. The final battle helped expose how far Khan had fallen, which made him even more tragic for me.
I don't want to say that Cumberbatch didn't do a fine job. I thought he did, though his take on the character was a little too cold and some of his emotions were overwrought. Some of that was the direction and musical score. I mean the music introducing him practically told you he was from the Legion of Doom. In Space Seed and TWOK I felt Khan's assertiveness, charisma, and arrogance more.