Will you eventually differentiate cultures' and species' combat styles? Some styles and armaments are especially effective against some other styles and armaments.
Let's say that a dwarven civilization fond of using heavy war axes and broadswords and wearing heavy plate armor is at war with an elven society using light armor and rapiers with bucklers. This would be an interesting feature if it varied from civilization to civilization, and moreover the elves would slaughter the big, strong dwarves if they managed to ambush them in close combat.
Will differences in diet and the wealth/comfort of a society eventually affect the strengths and weaknesses of its occupants?
A few examples:
A hypothetical society went through a period of famine lasting nearly a decade 40 years ago. Many of the current adults were children at the time, and their bodies would have been permanently weakened by nutritional diseases as a result. They could have decreased mobility, would certainly have lesser bone density, etc. Personality traits would also reflect this experience, such as the famed inability to let go of the 1930's Depression mentality many of us have encountered in older members of our own American society.
Some goblin tribes have been engaged in tribal warfare for hundreds of years (think Germanic tribes or Mongols), and have experienced an accelerated period of natural selection. The genes of those who were strong, intelligent, and early to develop and act sexually would have prevailed. Should they unite, they'd be a force to be reckoned.
A militaristic society conquers a sizable empire, and settles down to enjoy itself. After 3 generations or more, the values and strengths of the older generations have been lost. They may still have great technological military strengths (consider the stirrup), but their mental attitudes and behaviors would have deteriorated. They would lack developed physical strength and discipline, mental fortitude developed through important decision making and so on. Should a trying time come along, their luxurious lifestyle would surely make its effects apparent.
Can you give us some way of comparing beasts in our menagerie?
I know you want to avoid immersion-breaking features like "strength of 21, weight 220 stones, fat% 20, agility 15" and so on. But surely dwarves can look at one cow and another, put them through their paces, and get some idea of their comparative physical and mental attributes. The breeding system (which is pretty incredibly cool at first glance when considering its potential and all of the nice features you have built in like generational tracking) is rather useless without this basic ability.
I am sure when you get back around to agriculture you'll eventually address diseases and things like birth defects or genetic defects (hereditary blindness), so I'll forbear to add a fourth question today.