All good ones, Sean.
I'd like to see creature attributes that can be changed depending on the sex of the creature. (Horns for bulls, for example). I'd also like to be able to have creatures which can spawn similar creatures. I'm thinking Queen ants and Bees, here. Where they occasionally spawn a new queen, but mostly you get soldiers and workers.
I'd also like to see more reactions available at the smelter. The current number of free slots is too limiting.
More variety in mineral placement. Right now we just have small clusters, large clusters, and veins. I'd like to see several sizes of clusters and several sizes of veins. How about mineral veins that reach across the entire map? Short veins, with only 10-20 blocks? Medium clusters with 40-50 blocks, instead of just the 5 or 500 options we have now.
I'd like better control over the metals and materials used by civs. I'd like to make a stone-age civ that just uses basic wood and stone weapons. Bronze age civs are desired by a few people, I know. For my mod, I have lots of new materials in place, and I'd love to be able to tell my civs to use them.
Equipment for non-civ creatures. I want ogres using clubs, mail-clad Titans with gigantic two-handed swords, lizardmen using spears and leather shields.
On Sean's topic of setting values for wood and stone, I'd like to be able to access the default damage/armor setting. Right now it's 50%, which lets you do ridiculous things like kill someone with a sock. While cool, it's pretty silly. I'd like to be able to set that to a lower % (like 5), and be able to set everything higher. Maybe even have defaults by material? So, say, cloth is 1%, wood is 40%, metal and stone are 50%, and so on.