The thing is, combat qualifications in Star Trek are all invisible. We can't tell by looking which ship has stronger shields, more powerful phasers or faster warp or impulse engines. Maneuverability is not visible, either, and a big ship might well out-turn a small one.
count the number of weapons ports, but this has never been a factor in Star Trek, as no ship ever fires a "broadside" - a very low percentage of the guns firing is always plenty enough.
But in ST2:TWoK, such things should not matter. It's a battle of wits, Kirk vs. Khan, and it would make dramatic sense for the ships to start out more or less even, then to suffer damage, and then be repaired to again be more or less even - but Kirk's repairs are more clever, and with his "partial main power" he can escape Genesis while with Khan's "full auxiliary power" he would have been dead. Any "built-in" difference between the ships would be detrimental to the plot.