Pokemon became more inclusive to women with Pokemon Diamond & Pearl. Note that diamonds and pearls are typically things that are favored by Women. The Champion of Diamond and Pearl, Cynthia, is the first female champion in Pokemon. These games also introduced the pokemon Combee, whose female variant is more coveted and the only one capable of evolution. Half of the gym leaders in Diamond and Pearl are female, making it the first time the gender ratio was evenly split amongst Gym leaders. Interesting to note that one of the female Gym leaders specializes in fighting type pokemon, which not only is a first, but also subverts gender stereotypes of the different types.
I would conclude that all of this was done in order to be cohesive with the general ideology Nintendo was pushing with their DS/Wii hardware at the time: wider audiences, inclusive--their blue ocean strategy.
