I think that whatever one is the more dominant on a specific version, you'll get that one more often. In the case of Emerald, Illumise is more common so you'll have more of them hatch. As for LeafGreen, the female Nidoran are more common (you'll find males on Route 3 as well, although it'll take a while). There are quite a few Pokemon that show up more often in one version than another.