Those are pretty good ideas for handling breeding. I'm now moving to a system where you inherit the first two genes from the father and the last two from the mother, which should make the entirety a bit easier to control.
And I also added an example of what the gene results may be:
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Well not idea, you inherit genes from parents randomly but if they have same genes. dunno if you get from both it would make it faster, though maybe if both parents have 3 of required genes then there is only cases. where only one of parents have dud, which is not quite many compared to others. Because selection is still 2 and 2 but on the other hand it might make those parents with 3 genes easier. Btw liked new strapons after toying at friend's. Yes you can't early game get tier 5 genes. but it is probably ok, not something you need to mess. Same with domesticated trait. Though to get it leveling for class change is a bit sad.
Other things disliked in the end. Dislike how area control works. feel it spreads too fast. Just food for thought, make dungeons one time use, add special dungeons for leveling or tesing maybe at shrines later. (could give theming) What dungeons do. Have high area, higher tier dungeons have larger area. Dungeons increase threat level in area, again more dangerous and tier of spot dungeon is in the larger threat it generates in range. (Because as much as I was afraid threat growth would be a problem it does not grow as fast, heck unlocked everything and haven not reached threat lvl 2.) you can leave usual threat system because once you start knocking down dungeons global threat would drop and it would make it easier. Or make each pacified dungeon actually moves its local threat to global threat making natural progression of world getting more difficult as you antogonize it.) Threat is basically local threat level from dungeon+global threat level. Outoposts just supress dungeons in range with whatever pattern you want to keep them. (Current outpost fencing system works poorly because most of terrain is literally forests, leather, mountains, or other unbuildable terrain)
Books do not like as they are now, though idea is not really bad. My advice split what they can give up. So you are disincentivised farming shrine production or just raid same dungeon. So just take all dungeons (could make them even themed and designed for one time playthrough) so you get spread of dungeons. Do them all and you would get all books of wild. They disappear after completion. All books types give tech only what assigned. Books of wild(forrest) give some wood tech, Book of wild(ruins) maybe some magical stuff or technological or whatever you plan for ruins. Basic book unlocks basic tech you need, and to unlock better shrine books you need either pacify captured shrine and/or get proper book of wilds. (this unique approach might even help you theme dungeons a bit more later)
Off course set of dungeons would give same book and same book might have more than one tech to reduce work load. But this way you need venture forth for better tech to different dungeons instead of farming whatever lowest tier you have nearby. But now you can also target certain areas, or tribe dungeons to get certain tech. Outskirts of certain shrines might have more thematic to area tech which feels more correct thing and make starting a bit more interesting.(ok different start locations have different monster girls access and special resources I guess.) But I feel making more books and spreading over one time dungeons might make it easier. And If you need to add more tech you can add one more random genereated dungeon by theme or add it to shrine book, or add in boss dungeon, but I feel like there is more than enough of dungeons to give tomes giving core developments.
New crafting btw is interesting. Though again past certain point you become so powerful that replacing cloth of monster girls becomes irrelevant but again I never got past threat lvl 1 so having tier 2 enchanted troup is unfair. But actually letting player mess more with tier 1 equipment and try to gain access to new stuff as you progress to higher tier dungeons and areas is a good thing. Though again lvl 1 areas do not really need debuffing unless you want aesthetics.
Also like genetic replacement tribal therapy. You can breed and level up to certain lvl thesholds to replace certain encounters with ones you bread. At one point all lvl 1 encounters had quite high chance to spawn lvl 1 naked ratkin archer with 1 hp because I released into the wild quite a few lvl 1 archers while breeding. One way to shape your encounters ha-ha-ha. And because ratman archers is unnatural combination which came from human archer and ratkin It feels like fun things happened.