That's true, but MLB can control the schedule.
My feeling is make it as fair as possible rather than focusing on gimmicks like interleague play and intracity rivalries. It was fair before the wild card was a thing, and it could be fairer now. As zambonir notes, it would be easier to remove imbalances with 32 teams when and if that happens, and even easier if they are willing to stray further from the historic league definitions.