Most of the Captain's I choose for my fanfic are female, so I have no problems with women in charge.
I've fallen out with TrekLit of late, so I can't really say who is where and doing what, though I did love having Kira in command of DS9. Makes me wish the series had continued with Nana Visitor in the lead role.
Commander Austin Harris, First Officer, Deep Space Nine (by FltCpt. Bossco)
8.01 - Darkest Before Dawn
(Chapter 8 added, 12/09/2015)