I personally really disliked FemShep because of the voice acting.
Jennifer Hale only rally does two voices: strong, gruff female warrior, with a penchant for talking really low when shit gets real, and happy, flirtatious sweetheart. FemShep flips between both in the same conversation sometimes, giving me the impression that she's got bipolar disorder. That, and she sounds bored doing the lines, as she sighs with each and every word, especially when she's trying to sound gruff. MaleShep is more consistent, able to be gruff and tough, while still being able to tackle the more sombre moments well all with the same voice direction. Meer seems to be having fun with the role, while the same cannot be said for Hale, who delivers the same performance as she does in every role she's ever been in.
Also, you can create a more unique MS than FS. I've made 3 MS and 1 FS thus far, and my brother 1 each, and the MS all look distinct and different from one another, but the FS share the facial structures and features to the point where you'd think them sisters. Even the ones I found online looked similar, so it's not just a case of my brother and I having similar tastes.
That, and the final moment with Anderson feels thematically way better with MS, as there's a father-son-esque relationship between them. FS's scene just doesn't feel as good.