I hope you don't mind if I add my two cents here...
From what I saw I didn't look at Selene's sprite as being pigeon toed, and even if Pokemon does that stereotypical stuff with sprites (like the hiker sprite or the biker sprite, obviously) it's no reason to do that with a character that's important. Because all the bikers and all the hikers have the same sprite it's smart to do a stereotype because every single member of that group is being portrayed as that sprite.
Selene is a one-time character whose sprite only serves one purpose: to display a main character of the game. Perhaps she is pigeon toed, perhaps she isn't. To be honest I didn't think to hard into Selene's background to say that. This being said she is most certainly not the stereotypical adolescent girl. She's headstrong, tough, like misty (though thats a bad example because her sprite shows her pigeon toed xP) but she's not the cute teenage girl type that you'll see in May or Dawn.
Nevertheless, I don't quite see a pigeon toed-ness in her sprite. I mean I see where you're coming from but it just looks like her hip is popped out with some attitude there. When that happens its somewhat natural to angle your foot inward (well I'm not a girl but I have a sister and I've seen this happen )
I see no problem with it, if it looks pigeon toed to you then I guess Selene's now pigeon toed. So be it.