I think it's sort of obvious why they moved away from the ecoterrorism.
Terrorists who despise the decadance of the United States? Led by a guy with an Arabic name. Well, he turns out to be Irish
, but maybe that's a call-back to the 1980s, who knows... (good Irish roster of villains in that movie really).
You could say the nihilism of the Joker builds on this. We've had a villain who despises the world's decadence, now we have the anarchic embodiment of it. I'd be surprised if the third film doesn't have villains with similarly dark motives - Al Gore doesn't really seem to cut it (Item: Do we really need to portray environmentalists as the bad guys?)
And if you really want an environmental-themed villain, to me, the average schlub who just sees the movies and stuff, I'd have to ask if Poison Ivy doesn't fit the bill better. I thought environmentalism was her