They nerfed the inbreed + mutation strategy, which I think is good. It was a strange mechanic that kind of got around any risk in breeding and allowed for achieving perfect cats way too easily, along with stagnant gene pools leading to almost no diversity in your cats (kind of bad for a roguelike).
The issue is that they didn’t give an alternative, leaving endgame breeding in a tedious state. The main reason the mutation strategy was relied on is that stimulation and appeal weren’t enough. Strays are too weak and stimulation is too unreliable. This patch also makes the mutation furniture stat pretty weak.
Simply put, if they want breeding to move more towards a stray + strong cat strategy, they need to make strays good.
I think step one is just simply buffing appeal. You need way too much appeal to get decent strays at the moment. Step two is to make strays more mutated (it’s what really matters in the endgame and will keep the diversity up across runs). This can be done by giving a secondary effect of making strays more likely to have mutations to the now less-useful mutation furniture stat.
Finally, stimulation also needs a buff. Act 3 and on is pretty much balanced around all 7-stat cats, but it’s too hard to maintain at the moment with the stray + strong cat strategy. Stimulation buff would simply make it more reliable and consistent.
TL;DR: Breeding in the endgame is currently too much work, at a time where most people want to focus on the combat at harder difficulties. Mutation strategy was used to get around that, but the main issue is appeal and stimulation being too weak. They should buff those stats to make endgame breeding fun and consistent, without the need for relying on inbreeding.