It's a minor thing given how short the story was but the 'female' universe made use of a male Rand and male Marcus, and added in a male admiral i.e. added in additional males from the lower tier supporting cast, but then put no effort into featuring any of the female versions on the NuEnterprise. Of course by that point they had double the number of characters to fit in but even so, it's ironic that in a story where they could have featured total equality of the sexes, they still had a male admiral and still had three more men than women. Sigh.
Absolute numerical parity is a poor gauge of equality of the sexes. It rather smacks of tokenism. This two part comic book story is hardly a ground-breaking exercise in the promotion of equality of the sexes, but, within its scope, is rather a difficult one to criticize on that score (there are many other flaws more deserving of criticism).
Trek has had forty years to get this right and it is still very sexist - or at least sexist for what its supposed to represent. And while I agree that absolute numerical parity is unnecessary, what we have at the moment is usually tokenism. It's why you always get 2-3 women in the cast of 9 characters and why many other female characters are bought in as love interests.
But you're right. It isn't the main problem with this particular story (Jane Kirk takes the lead most of the time) and there have been improvements since the comic franchise began (we have a female captain featured in Khan 5). Nonetheless, I thought it was interesting to note the attempt to feed in as many male counterparts as possible in the female universe. They even had Chapel in her/his only speaking part to date