At the Risk of Starting an Argument...

[Curt Pangracs]

Pyros,

The problems you bring up should be easily overcome with a generic "terrain-layering" feature. The ability to layer the complete map in an initial, underlying terrain type (desert/forest/snow, etc.), then you would only need to change elevation, roads, urban and such. This would drastically reduce the number of hexes requiring individual attention.

Better still would be the option to select any number of hexes and apply any number of terrain attributes to those hexes selected.

More meandering here, but I'm not suggesting you scrap the entire auto-generation and other current mapmaking tools, just the possibility of adding some options.