It's a nice idea, and I have to disagree with Roxas on the basis of it being like Neopets--why should we throw out perfectly good ideas because they seem similar to what someone else is doing? I say, disregard them and go with what's right for Rescreatu.
With that said, I don't believe the gender differences are a possibility. The main issue being that many of the Creatu were drawn by artists who are no longer on staff. Since some are pending being redrawn, we have to ask ourselves: Would this be done all at once? If so, it would be years before all the Creatu are redrawn. Even then, petsite art has a tendency to evolve beyond what the staff originally set out for. So what I'm getting at is that the workload would be nearly doubled. I don't know about other artists, but one of the most time-consuming processes for me is the recoloring (to make all of the dye colors and whatnot). Having separated genders would mean doing another batch. D= *cringes at the thought*
Alternatively, you can always commission someone to make an edit or redraw your pet any way you like. Or you can just do it yourself with a program.