When we're on the Navy's boats, of course there's a formal heirarchy. But on our own boat, our rule is simple: the most conservative one "rules." If I want to reef, and he doesn't think we need to...we reef. If I want to run off downwind in a storm and he wants to heave to ... we heave to. Completely bypasses the who's in charge discussion to the benefit of the marriage.
Overall, we are at roughly the same skill level, with complementary strengths. I'm better at nav, he finesses sail trim. From time to time we deliberately switch up out of our comfort zones - for example, when we dock he generally handles the bow lines (greater upper body strength) while I take the helm; every half-dozen trips or so we trade for one. And that goes for galley cleanup too.