I think we should have some prevailing winds which the player cannot see but ultimately decides which biomes are created where.
I got my info from the wiki post about deserts, I may be repeating something that was already said but this idea was not in the wiki.
For example:
Mountains block these winds from passing any further, and thus create deserts as moisture cannot be blown in from the ocean/lakes to that area. In a similar manner one could create marshes, grasslands, etc etc. . . ...
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