It's a nice touch for those that prefer a female lead.
One of the very cool things about the 'Mass Effect' series, and BioWare games in general, is that your protagonist can be anyone you want. Well, anything you can create at least. Want a sexy female lead, guy that looks like John Waters or something in between? You can make it happen.
'Mass Effect 3' ups those options by giving you a choice in box art too. If you prefer a male Shepard, just leave the box as is, if your Shepard is a woman, flip the insert and you'll be represented on the cover too. Of course, these are the generic versions of the character, so unless you stick with default, it's not going to be the truest representation.
Still, the option is nice for gamers that want to keep their games on display and don't want to be stuck with one cover option.
Source: Game Informer