Part of the beauty of the Mass Effect series is that you can be whomever you want. There isn't a pre-ordained hero that tries to save the galaxy; you can make Shepard male or female, good or evil, gay or straight. "I'm Commander Shepard and this is my favorite Commander Shepard on the Citadel," you can say without a trace of irony.
Well, as open to customization as Mass Effect's protagonist is, the original Commander Shepard was female. On Twitter today, lead animator Jonathan Cooper said "Ten years ago this month, my very first anim test for Mass Effect. Yup, Commander Shepard was originally a woman," accompanied by a grey-scale animated image of her running.
Cooper followed up by stating that "I repurposed mocap from Jade Empire. Shepard was always planned to be both male & female after JE's pre-set characters." So, it was always the intended design for players to have full control over their commander, but FemShep was technically the first one made.
Remember how Mass Effect 3 came with a reversible cover that you could take out and flip over to FemShep if you so desired? Seems like maybe it should've shipped that way in the first place.