I think it would have been cool to see them use the blond one just because I can't really think of another example of a bad-ass blond woman in fiction... with maybe the exception of Charlotte from Samurai Showdown. (*sigh* I love Charlotte)
You could argue, I guess, that it's just an impression given off by the hair color that turns character designers away from it... but I don't personally believe that's the case.
My Shepard was always a redhead, anyways. I model her after a character of mine and name her Samantha. And I can't play the male Shepard because of the huge gap in the quality of the voice acting. But I don't need something that closely resembles my Shepard on the box, there's already a ton of badass redheads in stuff.