Tectonic Biomes

In real life occasionally pieces of plates get flipped over.  The fossil record reads backwards there.  At the same time you are adding a deeper world and more caves maybe you could create a sub-biome type.  It would be rare, but you could spot it because the stones and ores would be inverted, so the stones that should be at the bottom of the world could be at the top.  It could also come in an partially flipped section, so for instance the type of stone might invert for only a band of it.  In extreme cases this could mean a few surface biomes and some brimstone.  In less dramatic areas it might just create some nice banding.  Mountains might even have diagonal banding to indicate where one plate is riding up and the other is subducting.  

It's been years since I took geology, but you could weight certain stone types and features for certain biome types.  I don't know as there are any metamorphic or sedimentary rock types in minecraft but they could be added to give hints at as to how areas formed, which in turn could help you find specific minerals.  (You wouldn't need to implement it all in one go, but some planning now might make it easier to add more later.)