This can actually be accomplished in FTPro. It's just a matter of playing with the generation settings until things are close to what you want and then a bit of time manually editing the world in question.
Originally Posted by liborator
Not much to offer on this other than to take a look at where such resources are commonly located in the real world and try to extrapolate from there.
-populate resources around the planet (gold, silver, zinc, limestone... etc.)
FTPro can do most of this. Altitude, Rainfall, and Temperature are built in with quick toggling buttons. You can simulate a satellite view by using the "Show Other Shader" feature in conjunction with Bill Roach's Terraformer Package (also available from Profantasy).
-generate multiple map types (rainfall, temp, altitude satellite view, etc.)
Not sure on this one, it all depends on how inclusive you want a 3d map to be. I use Terragen to generate portions of the world map in 3d, but if you're looking to be able to render the entire world in 3d in a single shot, I'm not aware of any software apps that can do this other that Viewing Dale if I am correctly understanding it's capabilities.
-generate 3D map (would be great but not a must)
This can, in theory, be accomplished in FTPro via the Image Overlay feature. It's a bit of work, but can be done, though you'd probably be better off adding most of this in through GIMP or whatever other graphics software you have available.
-allow me to add towns cites roads etc. (if it added them to 3D map that would be amazing)