I think it would be cool if you could spend a significan amount of industry (similar to a smaller wonder) to dig a canal, each time you do it you lower the terrain by one level and mountains are not removeable. This way structures like the suez and panama canals would be doable in game. Probably unlocked during the industrial era?

You mean as a district or as a wonder ? I think that as a wonder it would make more sense, specially if it gave some sort of economic impact. However, I think that to integrate something like a canal would be difficult in this game.