Very cool ideas, I like the point system.
Erosion can already be modded into the game. You can make Mountains -> Hills -> Grassland/Plains. You can also set it up to include Volcanoes in the cycle, so that you have a very volcanically active planet where mountains (or jungle, for that matter) suddenly sprout volcanoes. In addition, volcanoes can erode (e.g., volcanoes -> mountains -> hills).
Some related ideas on the ecological plane of thinking:
Old Growth value:
Chopping a forest should give a value in shields related to how long the forest has been untouched. Old growth (virgin forest) should have the full value, with newly planted forest at maybe 1/5 the value, and growing over time. In addition, Forest/Jungle tiles should have tourist value that grows with each 1000 years it has been untouched.
Natural Wonders:
The idea of "landmark terrain" in Conquests is great, but should be taken a step further. Random natural wonders should be placed on maps that have tourism value, similar to a bonus resource.
More dynamic "global warming":
When global warming occurs, more should happen than just tiles losing forest or jungle. Ice caps should melt, and eventually the coastal tiles should rise. There should also be triggers for an ice age ecological disaster that causes ice caps to grow and tundra to encroach on other tiles (grassland would be the logical choice).
More events:
Similar to the very cool volcanic eruption and Black Death events, there could be other events generated in the game, such as drought, El Nino, hurricane/monsoon, tsunami, earthquake, flooded rivers, and positive ones such as overwhelmingly good crops. The evil side of me would also like to see Mad Cow disease, Potato Blight, and genetic disasters caused by too much tampering with the human genome after the discovery of Genetics or a major nuclear conflict. For that matter, a major nuclear war should trigger the appearance of Fallout II-style resources, like mutated cattle, salvageable military debris, and roving bands of refugees.
Splinter Civs:
This may not be the right thread, but we need splinter civs in the game. If your civ is doing really bad things (like pursuing a very ecologically-unfriendly strategy), you should have the risk of some of your cities seceeding and forming a rebel republic. Master of Orion III did a great job with this concept, where a colony in civil unrest would sometimes form an independent empire.