On the contrary, Shepard is THE best case to evaluate gender equality in the ME universe because we can see how this character is treated if everything about it is equivalent, except for the gender.
The result: There are a few specific characters, such a Harkin or the batarian merc recruiter during Garrus' recruitment quest in ME2 for whom it makes a difference but otherwise, Shepard has exactly the same respect, authority and general impact on and over others, no matter if they are men or women.
That kinda gives you all the information you need on the matter.
Now you may argue that this equality may be caused by game design and budged reasons, more than by a conscious effort to make them equal. Nonetheless, the fact stands that they are and that's that.
In that sense they do count.
But it's
because it generally appears that the intent is for 22nd century society to be equal that I think it makes sense to request more women leaders. I don't wish to constrain their artistic vision, but to encourage them to express it more consistently, rather than allowing subconscious 21st century expectations to compromise that expression.
There's nothing wrong with depicting an unequal society if you know that's what you're doing. But I don't believe that is Biowares intent.
I should also acknowledge that the current depiction isn't really incompatible with an equal society yet. The sample size is low, it could just be a matter of chance that these people are men. But that will become less plausible if such a trend continues.