I like your ideas, and would like to subscribe to your newsletter.
Particularly I'd like to see growers take a more active role in farming, and for larger farms to be necessary. I don't know how large a hectare or acre is in DF tiles (or, really, visually in Real Life), but I could imagine that a fortress of 200 subsisting on grown food would require several 20x10 plots, particularly if they need to lay fallow after a crop harvest. This could tie in well, in the case of underground (or even, for certain crops, above-ground) farming with flooding the plots to fertilize them, or to assist with growing - I am thinking particularly of the flooded rice fields you'd see in the southeastern asian countries. Growers would additionally need to spend time tending to the fields, making it a more full-time job (and tending farms abstracts well over DF's time periods).
I also like your idea of compost areas, and of meals leaving 'waste' that needs to be taken either to a compost area or refuse. This wouldn't necessarily refer to dwarven waste, but meal leavings like inedible parts of plants or leftovers. Likewise, as far as fallow plots are concerned, livestock can be used to graze fallow plots and help fertilize the soil, as I believe is used in real life farming as well. This may not apply with regards to underground farming, depending on whether muddied tiles will ever produce mildew/lichen, like surface tiles produce grass. Perhaps that could be the differing factor - on the surface, you can use livestock to graze and help fertilize, while underground you can flood the plot again. In both cases you can use fertilizers, like compost or potash.
As far as yields, as I mentioned, I like the idea that you need larger farms (and more farmers) to properly feed a fortress. Cooking yields, by comparison, can probably remain as is, maybe reduced only slightly, in order to help extend your stocks. Booze can remain as a cooking ingredient, but you should only be able to use it once, and probably only in lavish meals. That is, no cat beer cookies, or dwarven wine roast, comprised of wine/wine/beer/ale.
In truth, most of Arrkhal's posts could be copied toward whatever suggestion threads are directed toward improving farming, rather than making sieges more difficult.