The Biome Modification API is most often used for simple operations like add/remove/replace a feature/mob/etc., which, IMO, can be implemented as simple JSON files in data packs. Datagen can also be used, since most worldgen is implemented through data packs and datagen. In fact, NeoForge already has similar functionality and we can turn to its experience.

Idk if it is worth redoing the entire API or just adding the ability to create simple modifications via JSON files. I personally would not want to force the use of a datagen, since there are many simple mods that want to remain that way, although they can write a few files by hand + the current API may be difficult to expand. In any case, BMAPI is marked as an experimental API, so we have a lot of freedom and can indirectly opt out of some features.

I also think this is a great opportunity to unify the JSON file format with the NeoForge API

A data driven system could possibly be built ontop of the existing API to provide the common operations. I dont think we should be making breaking changes or removing the existing API. Even its made stable that does not prevent v2 module, or new additions.