They should have done one of two things. Cast Khan more accurately, or tailored the role to better suit Cumberbatch. Khan wasn't the only product of the Eugenics program. Khan was in fact said in Space Seed to be "the best of the tyrants". Cumberbatch could have been one of the worst of said tyrants.
I liked the movie, and this wasn't a deal breaker for me. But it just wasn't a great fit. And Cumberbatch was very good, he just isn't Khan.