More improvements to unimprovable/marginal terrain, perhaps in the modern era.
Mountain: Ski resorts, in the industrial age, adding commerce or hiking trails, adding happiness. perhaps every peak in the fat cross adds 1 health in the modern age.
Desert: Not sure - allow irrigation and give them a base of 1 commerce? Maybe windfarms or solar power farms, which can be used to add 5% more production to a factory? Allow towns, certainly - with sushi, for instance, you should be able to have towns in desert.
Jungle: Jungles are an incredible source of medicines now, so maybe medicinal plants can show up in jungles that add 1 health, but only if the jungle exists - clearing the jungle removes the resource, or the improvement can ONLY be made on jungle tiles.
Water tiles: Allow a waterworker, that can make improvements on water, like:
Fishing nets (+1 food) (with fishing), windfarms (like desert), offshore platforms (+1 shield), tourist attractions (beach, surfing, scuba diving) +1 commerce for coastal tiles
Change lighthouse to add 25% to trade routes or 2 exp points to naval units or something like that, or maybe add some events that can wipe out a net (like insects wiping out a pasture) and make the lighthouse reduce the chances of that.
Tundra: Probably nothing there, cause there are things you can do there.
More roading options: superhighway, which double road movement and adds 1 commerce, but also adds 10% unhealth (so you don't just spam them). Make rail add 20% unhealth (so again, you don't just spam them)