I am fairly confident that I've already, at some point on this blog, shared my opinion on this, but what the hey, I'll do it again. I prefer FemShep, and not just because I'm a woman. I mean that is part of it, of course, since female representation in video games is a touchy subject (see: Anita Sarkeesian's Tropes v. Women in Video Games series) that I feel strongly about, and it's always nice to play a character that shares my gender. I have played as BroShep and found the game just as enjoyable, but I connected with FemShep in a way that wasn't the same as with the male version. Jennifer Hale's performance was just top notch and played a major role in my ability to gel with the character; she just blows anything Mark Meer does out of the water, although he does, admittedly, improve by ME3. It also doesn't hurt that the gameplay doesn't really change just because Shepard now has boobs and a vagina, instead of the (sadly) default penis. Naturally, some dialogue had to be changed - like when Shepard goes to sign up as a mercenary to go after Archangel/Garrus and the batarian remarks that the auditions for dancers is in another location - and in the final game, Urdnot Bakara/the female krogan shaman, does mention that both she and Shepard should show the men how things are done. But for the battle scenes and most other cut scenes, not much is altered. She still punches the same and fires the gun the same. I know that this is most likely due to budget constraints because to develop different mechanics because BOOBS is a huge money waster, but I like that it was done this way. She is simply Shepard: a badass, survivor, icon.
I will say that I wasn't completely happy with the series when it came to the treatment of FemShep. It took two successful games for her to finally get her own trailer, because male = default in the gaming industry. And the lack of comparable romance options for her were disappointing, particularly when you get to the third game. I'll discuss this in more depth on Days 9 and 10 for your viewing pleasure. These, however, are only issues that I have with the creators, not with the character. Bioware usually excels at providing plenty of opportunities to play a female character (and not have it affect the game in any substantial way): Knights of the Old Republic, Dragon Age, and Neverwinter Nights**, for example. With Mass Effect's Commander Shepard, they did an admirable job at keeping with that tradition.
* Okay, I'm going to use Mwar's art on here as often as I can because she is amazing. I mean, just look at that FemShep!!
** I still play this on my PC. Probably one of my favorite games of all time.