I'll echo the general sentiments here. I didn't mind that they used Khan, I was a bit disappointed though because it didn't seem worthy of all the secrecy (especially when compared with how Iron Man 3 handled their villain). The replay of the scene from TWOK didn't have anywhere near the same emotional poignancy of the original. In fact, just thinking aloud here, I almost think it would have been better had the replayed another scene from TWOK - that of Preston's death, but instead of Preston it's Chekhov. As it was there was no drama to Kirk's death because Khan's blood had been telegraphed.
But the main reason why I felt dejected was because at the end when the Enterprise embarked on her five year mission...I really
want to see that five year mission! Two hours every three years isn't enough.