In contrast to this, ST:ID seems to be very explicit about Marcus/Khan possessing state-of-the-art 23rd century armaments. The extent to which these have been influenced by information from Spock Prime is unclear, but we do learn Spock has been spilling his guts on various threat issues, among these the existence and coordinates of the Botany Bay...
Just focusing on the Vengeance, it was a ship by order of Section 31 purely to fight/dispatch enemies, no facility for diplomacy or exploration.
This alone gives the ship builders much more freedom to construct a formidable combat ship compared to the Enterprise.
Then you have the superior intellect of Khan who had a hand with conceptualising advanced defensive technologies aswell as being able to work out warp related problems that inhibit greater warp speeds that normal human intellects could not previously resolve.