I think something we're all forgetting about is that Pokemon is technically a second party title, not a first. In general, Gamefreak has always seemed a step ahead of Nintendo when it's come to global inclusive. Pokemon had a playable female character by it's second generation (though late in the mix). In contrast, Fire Emblem (a first party title) didn't get it's official female option until it's 8th game in the franchise. Dixie Kong was added by Rareware, not Nintendo. And only recently have they begun to include a female option in non-spinoff multilayer Mario titles. And this is only accounting for sex.
This is a pretty good idea. My idea was for Rover to pose one of those awkward food analogies that villagers are so fond of for some reason, but have it vaguely relate to skin color. But are these cryptic questions really worth it? They're immersive, yes... but I think the novelty is wearing thin. I love your idea. It would be great to begin the game in, say, a washroom of the train (boat/whatever mode of transportation they want) and have a look at your face that way. Then you exit to your seat occupied by Rover. Perhaps his questions could then affect your map/town landscape rather than your physical appearance. This would give players more freedom with their avatar, while keeping them immersed in the introduction.