Does the new breeding mechanic play nice with egg-laying critters?
Females spend nearly their entire adult lives on the nest box, because if one clutch is gathered late or hatches she will instantly lay another clutch in that same box, and they can't have other creatures sharing rooms with them because if one of those extras steps on her nest box tile she will get disturbed and the eggs die. Because of this, every other clutch dies because when one clutch hatches the female immediately lays a second, and the hatchlings immediately disturb her and thus kill the eggs, and the player must micro-manage egg layers pastures to get them to breed at a reasonable rate, which means only females, or only one female, per pasture. But with this mechanic, a male must share a room with egg-laying females, correct? Otherwise fertilization will never occur. But then the male must immediately be removed...
If Toady didn't change behaviour to reflect change (breeding on touch instead of spores), I predict that some species will have problems with breeding (egglayers?...) and it will be significantly slower in some cases (grazers on any bigger pasture, anyone?).
Toady probably will have to address it after complaints of players.
I also wonder whether the new breeding system will play nice with egg-layers. In earlier versions, I studied the wiki and decided that birds were the best livestock for leather production, and kept them for that purpose. With leather in mind, I actively (and, with very few exceptions, successfully) tried to avoid harvesting the eggs, which involved disallowing them in both the kitchen menu and food stockpiles. To ensure continued reliable supply with minimal micromanagement under the new system, I would like to see either an option to revert to the previous breeding by pollen behavior, or a way to disallow egg-layers from laying non-fertilized eggs. This sort of thing would especially benefit elk birds, according to what I have read about them on the wiki.
On the "disturbing the mother" issue: Back in 34.11, I actually had eggs hatch after I had slaughtered the mother on two separate occasions (both incidents involved geese, if it matters). According to my admittedly limited experience, eggs hatched very consistently unless moved to a food stockpile. Then again, I was following the recommendations of using a battery farm, albeit without the doors (I left space to install them later, but the area was off to the side with no through traffic, and hatchlings that were free to wander were much easier to pick up and move to a different stall).
This might also be the place to ask about a way to "automatically forbid eggs laid in this box" so they can hatch (I seem to remember forbidding the nest box itself and that not working). Better yet, "automatically forbid eggs laid in this box, then un-forbid them three months after they get laid," under the premise that if they haven't hatched by that point they never will. An automated system could keep track of when they got laid much better than the player.