Hm, koff~
I like some of the starter Pokemon to be female. Certain Pokemon learn the same moves at earlier levels in their pre-evolved forms, so I can get the moves I want through breeding fairly quickly. I don't think I notice much. I don't really use 'gender specific' type Pokemon, so they could be either male or female. It also depends on how the male/female forms look. Sharpedo for instance, I like that cut on the dorsal fin, so I'd like it to be male, while carvanha is male or female. However there are some with the opposite, like my koffings tend to be male and weezing tends to be female, koffi~
Other than that, I have no issues with male or female Pokemon, as I need them both for breeding.