As has been mentioned before, Shepard is named after the first American in space, Alan Shepard. Given that a man was the namesake of the character, the only constant characteristic of our protagonist, it seems rather unlikely that the series was envisioned as having a female default. Customization and differentiation are hallmarks of the series; I suspect that the decision to have both genders available to the player was present from the start.
I'm surprised that so many people think that the reason Femshep wasn't included in marketing until ME3 was motivated by some degree of sexism. There are legitimate reasons that only Sheploo would be present in advertisements, it lends a single identifiable/iconic character to anything related to "Mass Effect". Male Shepard can look drastically different, yet you never see any other rendition of him (only default Shepard). It wasn't until ME3 that I suppose they realized that N7 armor could be the marketable image.