I think it would be great if we could built canals so our ships could cross that thin strip off land seperating two oceans, or get from an inland sea to the ocean.
Another thing: I would very much like the flag that makes it impossible to built cities on mountain to be exposed in the editor. That would (mostly) solve the ICS-tactic that the AI plays.
Quite funny actually: Firaxis has gone a long way to stopping the human players from using ICS, and now it's sometimes a killer seeing how the AI uses ICS
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Tundra and probably desert would be those terrains I would mark as "Can't contain city".