Best Captain: Kathryn Janeway -- there's something to be said for being psycho -- probably drank too much sugary soda
First Officer: Kira Nerys -- big chip on her shoulders for good reason -- We come in peace, fire the photon torpedos!
Security: Tasha Yar -- a little angsty but a good woman in a clinch
Doctor: Beverly Crusher -- most sensible woman they ever had on the show
Chief Engineer: Q -- if he can't fix it nobody can, besides, he'd be the token guy on the ship
Helmsman: T'Pol -- someone who can both steer and think for herself
Villain: Villain? We don't need no stinking villain! We got girl power! Babes in space forever!
I don't remember about Adm. Janeway being psycho or drinking soda. She is known to be a strict guardian of Starfleet Prime Directive and Codes even in the completely foreign Delta quadrant, and the foremost defender of crew safety. For that very reason, she deserves to be an admiral. Oh, and she loves pecan pie and tea, hates temporal mechanics as much as I do, and is more sensible than Bev Crusher.
I wonder why you don't mention Ro Laren. She's a far better helmsman than T'Pol. In fact: T'Pol never touches NX-01 helm: she is a science officer. Long afterwards, she becomes a first officer: a position Kira Nerys never holds. She is directly assigned as DS9 space station commander sometimes around the end of Dominion War. But she serves no starship at all during the war; concentrating herself helping her home nation Bajoran.
There is one TNG episode where LaForge consults a woman who designs the Enterprise-D warp drive. B'Elanna Torres is also a chief engineer. Her temper is what rules her out of my list. But technically speaking she's one hell of an engineer.
Female villain? You forget the Borg Queen?