I find it’s a shame not to try to improve its breeding logic and scenario.
Maybe it’s the free version that makes my judgement wrong, but with that version as advertising, I definitely don’t want to buy the game.
It is not advertising. In case you missed the disclaimer which can be found at the bottom of the starting game screen, it says the game will stay free once it's finished. Currently it is in development, and I guess the developer is mostly focused on coding while gameplay issues are put on the backest of back burners. That's why there are cheats as a palliative measure meant to eliminate the unnecessary difficulties.
For example, it is impossible to complete most of quests without the "infinite lust" cheat (else you just can't level up the offsprings in time). Quest rewards currently look like token payments. I guess in the final version of the game there will be some real awards worthy of the grind. Let us also not forget that the items system (be it consumables or equippables) has not been implemented yet.
As regards the trait system and breeding logic, I'd say you are taking it too seriously. Again, I guess the dev just did not take any efforts yet to make it look realistic, so in the current build of the game inheritance of traits is fully controlled by random number generator.
(Here's a tip: if you need to acquire an offspring with specific traits, especially a hybrid, breed at least 20-30 dams at once.)
Btw the dev admitted that some of stats such as Loyalty, Allure etc currently have no meaning and are only used as placeholders.
Some other stats seem to work at random, no matter what their description says.
Anyway, I agree with the rest of your points. Yes pregnant sex should be allowed to make training easier. The Homestead portal should be placed as close to the starting point as possible. Inheritance of characteristics should happen according to the basic rules of genetics. And so on.
And, of course, it would be nice to receive more quests related to the Blessed Nephelym (ending up with getting the frigid Emissary pregnant... that would make an epic "final boss battle"
).