I should not feel bad for Khan. It's fucking Khan, I shouldn't feel bad for him and his people. STID made me feel bad for Khan. Space Seed, TWOK, neither one made me feel sorry for the bastard. STID--especially the "should had let me sleep" line--had me cheering for the son of a bitch.
Fine, he's a genocidal war criminal, but they didn't sell that to me; they sold me a man that was centuries out of his time, viewed as being primitive and savage (why Marcus needed him, cause he thought different from the current people in Starfleet), and had his people used against him. He was someone that you felt sorry for, cause of what Marcus did to him.
I think having Marcus as the villain and trying to make Khan the villain too--based on his rep alone--might have been a mistake.