Problem can probably be attributed to betaness, but maybe add special monster attacks/visual elements/enemy drops that are either biome exclusive or just very common in its biome and rare elsewhere. When encountering the flesh or plant biomes it was pretty underwhelming to find them with the same enemies as everywhere else on the world and nothing else to do with them.
Yeah it seems to be the one downside with procedurally generated enemies. Hopefully they can figure out some kind of compromise.
It may hearten you to know that they are working on it. I was listening to the recent TehMorag livestream the devs showed up in and they spent a good ten minutes talking about how tailoring enemies to each biome is a feature of their plans, along with making enemies more different from one another and making worlds and biomes more unique in themselves (adding sandstorms, for instance).
I would like some hints on the story of some biomes. Like the underground gnome sub-biome. I see mini lamps and mini houses, but I just smash them for pixels. Nothing telling me what's up with that place.