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[General] Random generation dilemma

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Here is the deal, you have to make a map that is intended to be generated entirely randomly and is intended to shape into a form of loosely connected islands with different biomes spawning different objects appropriately.

How would you go around doing that ? My original intention is as follows:
Paint the entire terrain in alpha tile and cover the ground with a grid of regions.
Every region would have a doodad in its center (that would take up roughly 4x4 space on a regular grid) that would replace the terrain tile, these doodads would have multiple animations to be played with different texture for a different biome and would be set to a render-off state on the initialization.
On generation, some of these doodads would be shown while the pathing cells in their cells would become pathable.
In order to paint the shown tiles with a proper biome, a multitude of larger (pre-made) regions would be moved around the map randomly and an animation would be played for every tile doodad in that region to display the biome specific animation.
The only effort then would be to save which of the small cells was shown and which hidden in order for doodads and units to not spawn in them (as they would be spawned in a random spot in the big biome region excluding the pathing-off cells as then things might spawn in the "water") and to make sure the biome regions don't move too close effectively overriding each other.

Ideas ? Impressions ? How would you go around this issue ? Are there more efficient ways to do this ? Without using doodads as a replacement for the tile perhaps ?
Any feedback welcome.
 
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