How about only removing entire biomes that clearly have nothing built on them? For example, the entire desert biome where Vlad's new village is could be left intact, but the massive tundra biome to the north could be completely regenerated? The number of biomes that have absolutely nothing built on them greatly outnumber the ones that do. But I have a feeling that if a biome is saved this way and an ocean biome is generated around it, it would look odd. Or at least it would look unnatural.
I have a feeling I'll start playing again when 1.7 is released. I'll rebuild the Iron Farm, and I'm feeling optimistic this time.
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