Chekov was first officer of the Reliant and Spock was captain the refit Enterprise on a cadet training mission. As you stated the films always wanted to reset everyone back onto one ship namely the refit Enterprise with the exception of in TUC
Sulu was captain of the Excelsior. I think it would have been more interesting if in WOK
Chekov was the captain of the Reliant and in TSFS
Sulu was already given the captain's chair of the Excelsior.