One thing I'd like to see is the effects of critters on trees: Elephants could eat trees-or atleast strip them of branches, while other critters (ants, termites, tree snakes, mandrils, leopards, elves, etc.) could live in(side of) trees.
Trees and other plants might additionally have diseases, and be homes for/infested by, vermin.
Also, I feel it would be appropriate to feature more prehistoric critters in the game. Maybe not dinosaurs (except in certain "rule of cool" circumstances?), but things like cave bears, mammoths, etc., that were around when humans and other hominids were around.
One popular theory about the extinction of mammoths, and various other "recently" extinct prehistoric animals, is that humans did it. Maybe in the DF world, it never happened.
Maybe there are extinct animals that don't exist as living critters, running around as undead?
Also, could we see biomes shifting? Possibly after major geological events?
If a volcano erupts, it might cause the biomes around it to repattern themselves. Deserts might move in to cover formerly verdant areas, and forests might in turn cover plains. Obviously, glaciers might move.
Biomes themselves might have subtypes, with their own distinct populations, and possibly separate features. The oceans around Antarctica are different from the oceans around the Arctic Circle. They're both arctic oceans, but at completely opposite points on a globe. The Hawaiian rainforest is different from the Congo, and from the Amazon Basin. The Australian Outback is different from Death Valley, but they're both "badlands", etc.