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Well, consider Khan was a man of the 20th century, and he nearly pulled off the greatest heist of the 23rd century. If you were an ensign on the Enterprise, and you wanted to take it for a joy ride, you probably wouldn't even know where the keys to the ignition were. Khan figured it out.
When Khan first recovered from hibernation, he was given access to the ship's technical data which is what allowed him to learn to take control of the ship. He didn't just figure it out. He had 72 other geneticly enhanced ubermensch to help him as well. Taking the Reliant is likely similar to taking the Enterprise with the added advantage of having the Captain of the Reliant under mind control.
Khan was a formidable adversary, but don't overestimate him either.
OK, imagine giving the technical data of a Tesla to 72 Model-T mechanics and tell them to figure it out. It's not going to happen in a few days.
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