2)Kirk V Kirk
One of the strengths of Space Seed and Wrath of Khan was the dynamic between Kirk and Khan. You had two characters that were a good match. Their character traits complimented each other and it provided them both with a real challenge. Even though you always knew Kirk will win, Khan was not going to be an easy foe to defeat. In Wrath of Khan, after their first encounter, Kirk states that the only reason they are still alive is because he knew something about the ships that Khan didn't, i.e the prefix code that lowered the Reliant's shields. It was Kirks' three dimensional thinking that ultimately led him to victory over Khan's two dimensional thinking. Kirk in the original series was a proven captain. He had demonstrated that he was a born leader and his crew trusted him. He could be cocky and sure of himself but he had leadership skills that balanced that out and kept it in control. Pine/Kirk in JJ's Star Trek is an almost polar opposite. He's miraculously found himself promoted from cadet to the captain of the federation flagship after barely completing one mission. He hasn't had time for his skills to mature and show he could make a good counter to Khan Noonian Singh. Khan is super intelligent, has super strength and was a dictator that ruled almost a 1/3 of the Earth before he was overthrown. Kirk in Star Trek (2009) had shown no interest in excelling in Starfleet and has yet to prove he is a competent captain rather than someone who accidentally fell in the captains chair by luck. Kirk doesn't have the experience to be a credible opponent to Khan and therefore this Kirk V Khan will be a very uneven match and the confrontation will ultimately be less satisfying. Again it will not be able to better what's already been done.