I also agree with Eddie that natural barriers like mountains should be natural barriers to everything but explorers perhaps without a highway or railroad built on them. A band of people geared to settle a town (settlers) sure aren't going to be hardy enough to cross a nasty mountain range on their trip. They've got to find a river, road, or lowland way through somewhere. I don't even think military units should be able to cross mountains, and maybe not even hills.
Engineer units could be returned as a proper military unit to more quickly than usual build roads in front of advancing troops, like Hannibal crossing the mts. with his elephants. Engineer units could be good for running into enemy territory and pillaging improvements or blowing bridges--they could move 2-3 spaces per turn and ignore any zones of control. Big battalions of anything from spearmen to knights to tanks are not going to go wandering over hills and mountains in rough enemy terrain. They are going to stick to lowlands, open areas and roads.
Of course, come to think of it, this takes away entirely the fun and strategy of defensive advantage to hills. Maybe only foot soldiers could climb unroaded hills, but not mounted or wheeled. Good for defensive positions and pillaging...not helpful to sneak an army of cavalry right up next to a city along a mountain range.
All said, I really like the idea of natural terrain being much more of a natural barrier and border. More borders would naturally establish along mountain and hill ranges where settlers., explorers, and units in earlier history had a hard time moving beyond and could not readily expand beyond.
I haven't played with the game editor before. How hard is it to change tile accessibility to a terrain type for any kind of unit in general, and also based on whether the terrain has a road or railroad? Would it be possible to modify rules and map to force one to build roads over mountains to get settlers and units over?