But some technological progression happens. The Mirror Universe, the NX-class are practically warships. The Uss Defiant (Constitution class) from the Prime universe, Ahhinilated every warship that opposed it. And the Defiant was an explorer, not centered on battle.
And that's what the story writers wanted to happen. Let's throw in a TOS ship back in time/another reality and see it tussle.
And in STiD, they wanted the Vengeance to be outright superior to anything the Federation had at the time, so much so it would put NuKirk into a situation where he felt powerless, one of the main themes of STiD is that Kirk wasnt ready for the chair, the Vengeance is another story device to demonstrate that.
The JJ era ships clearly look superior to the TOS counterparts, then throw in Khan's contributions, his intelligence levels and ability to learn and solve problems beyond a normal intelligent human could, then backed by a mandate to build a no compromise battle ship, there is a convincing case for the Vengeance to be that advanced and combat effective in 2259.