That's already implemented: why do you think Dwarves leave seeds on their chairs when they're done eating?
Hahahahaha!
About the idea of requiring fertilization in general, though:
Frikkin' great idea!!! I'm all for it!!! And it doesn't need to be poop, though it would probably be the best... And potash can already be used as a fertilizer, though potash only provides one of the major crop nutrients. Potash provides potassium, though other fertilizers would be needed for providing the other two major plant nutrients, nitrogen and phosphate. I doubt, though, that dwarfs in the setting of DF would know about nutrient requirements of plants in so far as individual chemicals are concerned.
According to a brief, uncited blurb in the fertilizer article in wikipedia (
http://en.wikipedia.org/wiki/Fertilizer#History) even slag and cinders were used in fertilizer, which would be dwarfy. However, the wikipedia articles dealing with fertilizer are woefully lacking in citations as well as history prior to the agricultural revolution. I will need to research the history of fertilizer some more.
Also, about desert and tundra fortresses being effectively screwed: so what, says I. It would make it more challenging, more realistic, and spice up the game in a way that isn't introducing some arbitrary, contrived game mechanic for the sake of making the game more complicated. Deserts and tundra are too hospitable as is, anyway, methinks, and if this game is setting out to be a simulator of civilizational/economic development and siege warfare, better simulated farming is a must. Plus, if more realistic crop management is included, it's not like it couldn't be made to be turned off by the user if it's a possible game-breaker for those who don't care as much about the simulation aspects of the game, which is understandable.
As for introducing poop in general, I think it should be done, eventually, I think. But that's a whole different thread right there and the AI is not going to be good enough to effectively implement that for a while...