On paper Khan and Spock are a good matchup, but ask yourself, do you honestly see Spock or Khan defeating the level of characters that Captain America and Deathstroke have faced down? Cap and Slade routinely take on characters waaaaaay beyond their weight class and sometimes TEAMS of them and, not only do they come out on top but they make them look like chumps more often than not. The TREK universe simply does not have characters of a superhuman caliber for Spock of Khan to face on a regular basis. In the Trek universe, Khan would be considered a Super Human but by DCU or MU standards, he's pretty low level. Heck even DATA of TNG would be considered low end Meta by those standards and he is probably at the top of the TREK universe scale that we have seen.
Experience fighting much higher end superhumans makes a HUGE difference in my book.
True, but Spock still very skilled, and probably equal to steve physically, and Khan is enhanced like slade isalso!