If I remember right, they were going to give Chekov a Captain's rank in Generations, then thought better of it. Probably figured everyone would ask "then why isn't he the one commanding the Enterprise-B?"
Actually, Chekov was a last minute addition to that film. Every line that Chekov had was supposed to be for McCoy, but De Kelley declined to appear. But Walter Koenig agreed to do it, so Chekov was put into the film and got every McCoy line.
Same goes for Spock: Nimoy didn't want to do it either, so Scotty got all the lines that Spock would have.