I realize that Nero going back in time changed things, but it doesn't explain why everything changed. For example, Nero going back in time somehow made Chekov a super-genius?
Nero and Spock didn't go back in time as much was they went backward and sideways
. They entered another universe. Nero's actions did influence some events but not all. And Chekov was always very intelligent. He frequently manned the science station in Spock's absence. But yes, any differences in the two Chekovs would be inherent differences in the two universes, not from anything Nero did.