I've got some ideas about farming.
As far as the metal mechanisms idea goes, I think it's a good one, except I think we should be then given the option of watering our crops by bucket - a slow, ponderous, and wood-intensive way to go about it, but I don't trust Nile flooding.
As far as floodgates go in the first place, it's never seemed to me to be particularly logical or realistic to have a lever system like this at early stages, especially because it functions through several layers of solid stone. If you ask me, you should just be able to open a floodgate by hand, and then just enough to let out a little trickle of water to wet the ground enough for mushrooms (and then open it all the way later to drown the invaders). Having a dangerous quantity of water getting just sucked out of the room by a shut floodgate isn't realistic in the first place. Possibly this is due to the lack of a system of elevation in Dwarf mode; the concept of water flowing downhill breaks down when...there...is...no...downhill...
A miner with more skill should be able to open a channel right to a body of water (i.e. no floodgate) with less chance of getting caught in the flow like an idiot. I don't know if this is the case already, but in my experience it doesn't seem to be. Also, the concept of a simple dam that can be destroyed seems logical to me as well.
In addition, we're told about rain so often that we should be able to goddamn do something with it, like set buckets to collect it or a channel to bring it into the fortress.
The idea that dwarves shouldn't be able to build channels outside is illogical, if you ask me. I mean, all balance issues aside, it's a ditch. I'm sure the pathfinding behaviors that make channel corralling so effective will be corrected eventually or made harder to use (i.e. an animal who fails to find a path because he's been cunningly trapped becomes skittish and/or violent). Of course, channels must be made correctly or there are all sorts of ways to muck it up; that might be an effective way to discourage it, too. A risk of accidentally diverting the main flow of the outside river toward the cave entrance might be interesting...