Our house has two master suites, but they're not "his and hers". In our case, the entire second floor is the genuine master suite (ours). It's a huge room with a huge walk-in closet, dressing area, and large bathroom. On the first floor, there are three bedrooms, one with a private bathroom.
We gave the downstairs master to our boys, figuring they'd share, and the girls also shared a bathroom, but had their own rooms. Older DD has been gone 95% of the time at college, and doesn't plan to move back home. So, DS11 has taken over her room--we knew this would happen, she even let him pick the wall and trim colors. So now DS20 has the bed/bath all to himself. We figure, down the line, we could live on the one floor.
Beyond special circumstances, as some have mentioned, I can't imagine giving the master suite to a 6yo. It sounds like a great way to raise an entitled little snowflake, though. Have they ever seen "Mean Girls"? The Queen Bee sleeps in the master bedroom--"It was my parents, but I made them trade me!"