I desperately miss seasonal flooding. The mechanic gave such character to the farms of your fortress. Optimal plot designs would cling to the sides of the winding cave river. Sometimes the cave river would split, and you could use the middle island as a safehouse, if it was large enough.
I miss the 3d version cave rivers, too, since they would often go undiscovered until you took it upon yourself to dig some gigantic project, and their discovery was such a surprise! Their path through the mountain rock was often chaotic and unpredictable.
You could argue that certain animal behavior was removed or changed. Think the rage-filled elephants from Boatmurdered or the deadly carp from the early 3d versions. These creatures aren't GONE gone, but their behavior has changed that they might as well be entirely different creatures. Sure, you can call it a bug-fix, but in the realm of DF the line between intended behavior and interesting gameplay is pretty damn murky.
Kobolds used to be more common, but I think their civilizations have trouble surviving in the most recent worldgen and you only see them occasionally.
I think certain animals are over-present in recent versions. Think about the last time you embarked on a hot savanna river and there WEREN'T just hippos, alligators and eels. Sure, new animals eventually wander on, but chances are you see the same damn creatures for years and years. I remember old versions having a more diverse faunal presence.
At least we still have Gnomes! I remember a fortress where I caught and tried to breed the little dudes. I thought the little 'g's were awfully cute. I can't remember if I succeeded but I know the map is on DFMA.