As for genetics and breeding:
You already track who are the parents of an creature over this you can calculate the
Inbreeding Coefficient of an individual.
Depending on this indicator you can determine Birth and genetical defects.
Give in some random Mutation modificator now and then for a treat and you can incredible powerfull yet even almost new animals by breeding. The Downside would be that you need for an an healthy outmaxed race an very big breedingbase or very clever technics of breeding like rotation breeding. More information on this you find under the names "
Genetic bottleneck",
"Founder effect", and the artickles related to them. hmmm best you would start at
Population Genetics.You can also take in account failurebreeds by bad decissions. An creature only trimed on strenght would have problems with longtime work, stress on the skelleton, highered aggresivity, more food usage etc.
Eugenetic i think would be on the long run deadly for any DF race as the sittuation is now cause the breeding stock is from beggin with a bit small.
And can you make the worldgen an bit more stable by moving some parts of its Data on the HDD as long they arent needed? I got some crashes on longtime gens (2000 years+) and i think thats cause of the number of creatures and events. I dont know how it is done internal but i asume you hold all creatures and events in the ram at any given time. While its very logical for the lifing many of the dead arent needed i think and also long gone wars wouldnt be needed either.