One of the most important points made so far is that different DF players like very different things, and no new feature should limit a player's ability to make fortresses in savage evil areas, wage war with every race, or live in isolation (though I would be fine with making it much more difficult to embark in a desert or on a glacier).
There are a few ways to make those playstyles easier, such as adding more control to the flow of migrants and merchants. I would like to see a feature where you can choose between (1) the current system where peaceful outsiders enter the region at will, (2) peaceful outsiders notify you of their presence outside of the region, and wait for permission to enter before giving up and leaving at the end of the season, and (3) peaceful outsiders are automatically turned away before entering the region.
On the agriculture topic, in the OP I tried to emphasize other topics because while the farming system is an incredibly important topic, it has already been heavily discussed already, especially in terms of the size and yeild of farms. I like the ideas about crop disease and health/happiness benefits from varied diets because they add an optional layer to farming/trading, though, and they would be fairly easy to impliment.
With the underground ecosystems, I tried to make an underground plant that could only survive at very high temperatures (near magma), but that isn't possible right now without memory hacking. I would love to see something like that added to the game. Given the amount of magma on each map, I think it would be believable if plants like this justified about half of the underground fauna, and some basic underground soils. I am comfortable with some magic sustaining the underground as well, and I'm sure some more specific magical justifications will eventually come from Toady.
I'm sticking with my ideas on different civs having different specialties, though. The highest levels of craftsdwarfship should come not just from an individual's practice, but from generations of passed down knowledge and experience. Aside from possessions/moods, the highest quality goods should only be produced when high skilled dwarves move into your fortress, you send your aspiring learners to the experts in other cities, trade, or having an industry in your fort for a *long* time.