It really depends on what kinds of characters they are. Frankly, if it was in someone like Dawn or May's point of view, I may bite off my own tongue rather than endure having to read that story. If it's a GOOD female main character, then it wouldn't be so bad. As long as the character has some personality and flair, and isn't just the generic, random saint, the gender isn't really that big of an issue.
As for starter... Do you mean out of the ones availible in the games or out of any Pokemon? If it's the latter, then a male Nidoran. If it's the former, then I don't really care enough to have an opinion.