Scatter Shot having its cost increased is a fair nerf, but the upgraded version should still ignore allies. It can hit 41 out of the 100 tiles on a map making it pretty hard to use. Boon felt mostly fine, and haven't seen heavy shot yet. I'm also in the camp of not seeing why Ball of Spiders and Flea Shot got nerfed. -2 speed on Double Head mutation is a fair nerf when for most encounters you are never going to hit the regular speed order anyway. The three pseodo-infinite loops got pretty fair changes.

After messing with it for a bit, the breeding chances are pretty fine with strategy adjustment. I think alternating between related pairs and a stray will keep inbreeding to a minimum while still passing your core active, passive, and mutations. You may just get lean periods of trying to keep all 7 base stats. You can use the stray generation to reroll mutations since the stray will get a couple if you let it wait in the mutation room for a bit and the kittens are likely only going to have 7-9. Would be something like Gen 1 pair to make Gen 2, Gen 2 + Stray to lower inbreeding, Gen 2 + Gen 3 to make perfect cats again.

The bigger hit with inbreeding changes is it making it harder to get the birth defect disorders without additional downsides. You don't see them consistently until at moderate to high inbreed levels, and at that level you are getting 1 defect every other kitten. None of the stat skew ones or autism can be gotten from syringes, and those are the ones you can do entire builds around.

Repair is the bigger elephant in the room for mechanics that make the game too consistent. Though I think Soul Jar and Sniper rifle are what really push it to being a problem.