It's not clear when the Eugenics War were. We have the late 20th century (TOS, TAS), the mid-21st century (ENT), or the mid-22nd century (DS9).
I understand why the comic series leading into this film didn't give information on the discovery of the Botany Bay.
However, why didn't the film include this information and show the betrayal, as seen from Khan's viewpoint, in a flashback?
I have issues with the USS Vengeance
; namely, the issue of a covert black ops unit using this behemoth. The purpose of such an unit is stealth - you don't want to draw attention to your activities. This ship is contrary to the nature of such an unit. Excuse me, here, if I offend, but it is as idiotic as planting bombs in a camera-heavy public area while wearing your trademark hat in your trademark style.