I've read the development plans thoroughly, so forgive me if I somehow suggest anything that's already planned; I just somehow missed it.
My first suggestion, and probably the least work intensive, is fences; or, if you'd like, fences if made of wood or stone and railings if made of metal. Essentially walls that you can see 'through' (technically over, too) and that stop animals small enough (and babies and children) from bypassing them, and that even dwarves and other humanoids have to take a bit to climb over rather than just walking through. Elephants, of course, being monsters taken by insatiable bloodlust, would merely crush most fences underfoot.
These would be nice for, say, keeping livestock from running everywhere, or perhaps putting a railing along the river, chasm, magma, or pit to buy dwarves who were ambushed by monsters from them time to run like bitches while the creature (probably) scrambles over the fence.
Second; damming and channelization!
The latter is, really, more important (to me) and so we shall start with it; if you link up two river squares with a channel, it should, IMO, essentially transform into a river square, complete with fish (and everything else that comes in a river, lol lizardmen.) This would allow dwarves to straighten the river or even the magma, making the idea of farming or living or working among its' banks much easier to engineer.
Third would be damming... the ability to stop the flow of the river in a certain place by placing floodgates along the flow downstream. For instance, in the process of channelizing the cave river, you could dam off the places where it winds (and comes out back into the channelized straight, probably), ceasing water to flow there and creating a dry - or more accurately muddy, at first - riverbed. And then, once dechannelization is in, you could fill in the river bed, or just do with it what you would.
Along with this, of course, would probably necessitate measuring jsut how much water is in any one body of water, which of course could mean an end to the good old 'oh why you pulled the lever and now the world is flooded because the river is made of infinite.'