If there was one thing I'd want to add, it would be more realistic genetics. Different sizes, colours, patterns, all based on real genetics for that animal. There's already a little taste with albinism in the elk and kind of with the wild grey pigs with the larger variant.
I just like the idea of being able to selectively breed animals for multiple purposes from the same " source " animal/species.
It might be easily abused depending on how it's implemented, but at the same time, it could be very hard or even impossible to get the " perfect " domestic animal outside of cheats ( not unless you spend several years in a world ) since you'd have to find animals with these genetic traits, and even breed and test to see if an animal may have a desirable recessive trait in the first place. It would be a very long standing project, but I feel it could make the domestication process a lot more interesting and interactive. There's also room to being penetlties for inbreeding, like animals being weaker, or more prone to sickness, or even have the ability to just die on you prematurely as opposed to animals that would live indefinitely if otherwise healthy. It could also add some interest for multiplayer servers with interesting coat colours and patterns for animals like rabbits or chickens, maybe even extend it to wolves and foxes, to keep around as a sort of pet. It doesn't even have to stop at livestock and pets, pibald deer are really pretty. It would also add interest in taxidermy with the different patterns and colour and also sizes.
I know that they want to work on a more interactive system with husbandry, but I doubt it'll ever be implemented like this. So yeah, this is what I'd add to the game if I was given full rein and full freedom. Other than that, I'd add trains. I could not tell you why. I just like VS could do with trains. I doubt they would get used all that much though m, at least in singleplayer. they'd probably be very resource intensive, but they would safely be able to take you from point a to b in a relatively fast place. again though, the resources it'd probably take would probably make then not all that useful unfortunately. still, I would like them.