R/B/G/Y gave us our foundation for what Pokemon and that world.
G/S/C added onto the foundation (with things like Pokemon genders, shiny Pokemon and breeding)
R/S/E took introduced Jhoto ideas and made them more complex, with things of Pokemon characteristics, abilities, tougher breeding rules and the 2VS2.
D/P seems to be sandwiching on those previous ideas and making the games more difficult for players. Pokemon gender differences will most likely make breeding, battles and training much more difficult for players, so I see no reason why it should be left out anime-wise.
An explaination as to why we're seeing the gender differences now could be very simple. What I was thinking was that with every new region Trainers visit, new aspects of Pokemon world are steadily introduced to them. You can't just be in one area of the world know EVERYTHING there is to know about the world around you. A peron needs to travel and experience different thing in different places.
Prof. Oak could say that the reason Ash never noticed the differences before (really, the reason we never SEEN the differences before) is that only Trainers of a certian degree (also coinciding with Trainers who are visiting Shinou) are introduced to much more complex aspect of Pokemon.
That sounds a little an easier pill to swallow than just saying "Oh, those Pokemon differences are onlynative to Shinou, period."