I think the nether wastes should be the only biome spawning fortresses, otherwise I think it is nearly completely useless. To account for the fortresses lost with this change, there should be somewhat more fortresses in the wastes. Furthermore, fortresses should be unable to branch out into other biomes(the game will be forced to put the part of the fortress somewhere else). Also 2 minor changes: whenever the fortress ends, there should always be an end segment(the "broken" part at some of the ends already) and whenever the fortress cuts through itself, air blocks should be generated.
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