Personally, I think a lot of people still find the idea of something that falls into both sexes to be really disturbing. I wouldn't deny that there are tons of things in nature that fall into that category (as Myles said). Likewise, there are just as many creatures that can switch genders as needed (some frogs and other amphibians can do that when the amount of suitable mates dwindles in certain regions of the world, if I recall).
However, the issue of things being age appropriate for children easily would keep these things from being introduced into Pokemon. Granted, there are a lot of older fans into the series (though even I at twenty-four find prospects such as these things quite disturbing, even after educating myself on such matters), but unless Nintendo wanted to lose a ton of customers who's parents are upset with the content of their video games, it wouldn't be a good idea to include these...