Here's what I think would make a good set of 'Terrain Modification' additions, in rough chronological order:
Irrigation - available with Agriculture, but only for Plains, Flood Plain or Grassland tiles with Fresh Water (River, Lake) adjacent to the tile. Adds + X Food per tile, but requires Gold maintenance each turn, like a road.
UPGRADE: with Engineering, can build Qanats, long range Irrigation systems: require longer construction time, but can provide + X Food to Desert, Plains or Grassland tiles up to 2 tiles away from a Fresh Water source. Still requires Gold per turn for Maintenance.
Canal - available with Masonry, BUT only up to 1 tile long, only through level (Plains, Desert, Grassland, Tundra) tiles. Allows Ships and Cargo Ships (Trade Routes) to move/be traced through the canal.
UPGRADE - with Steam Power, can build Locks, now canal can be built through Hill, Marsh, Plains, Grassland, Desert, or Tundra tiles for up to 3 tiles long. Requires expenditure of a Great Engineer to start, long construction time for each tile, 1 Iron resource for each tile.
Reclaim Land - available with Machinery, allows coastal tiles to be changed into Marsh tiles. Coastal tile must be adjacent to a land tile that is Plain, Marsh, or Grassland. Requires expenditure of a Great Engineer for each tile converted.
Tunnel - available with Gunpowder, allows Road OR canal to be built through a single Mountain tile BUT requires expenditure of a Great Engineer to do so.
UPGRADE: - available with Dynamite, now Tunnel can be built for Road, Canal, or Railroad through up to 2 Mountain Tiles. Requires expenditure of a Great Engineer to start, long construction time for each tile.
High Bridge - available in Modern Era (approx 1935 - 45 CE) Expend 1 Great Engineer, build a Road or Railroad across 1 coastal tile. Ships may still use the coastal tile for movement (think Golden Gate Bridge) Requires 1 Iron resource
Chunnel - available in Information Era, Expend 1 Great Engineer per tile, can build up to 2 tiles of Undersea Tunnel through Coastal tiles which include a Railroad in both tiles. Ships can still use the coastal tiles for movement.
Artificial Island - available in Information Era (+ 1990 CE). Expend 1 Great Engineer, build a singe tile of Plains on a Coastal Tile, which does not have to have land adjacent to it already.
I would suggest that since these are all changing the 'natural' terrain, they would all extract a Maintenance Cost, like a road or railroad. You are, after all, keeping canals and irrigation ditches dredged, low-lying land drained and dammed, and major steel structures (locks, bridges) working all the time.
I am debating requiring a Great Engineer be extended for basic irrigation or canals - historically, it's not really required, but perhaps requiring you to have a Great Engineer for each project, but not expend him, would keep gamers from starting canals and irrigation projects everywhere all the time. You could start only 1 for each Great Engineer, and he would not be available for Wonders or anything else.
Because of the complexity and cost, the late-game Canals, Tunnels, High Bridges and Artificial Islands should all require expenditure of a Great Engineer AND construction time similar to a Wonder or National Wonder.