Here’s my personal perspective …
First, I generally like breeding. I think it is mostly good, but could surely use a couple quality of life tweaks.
With regards to recipe drops, I think the themes within creature races are useful. If I like the first Salamander I found, then it feels cool to get a recipe for another Salamander, because there is a good chance that I like it as well. In most cases, I think the first creature you find is a good representative of the race. However, there are a few exceptions … For example, the first Centaur I found in the Realms was the Centaur Duelist who is weird and doesn’t really do anything early game, which makes it hard to get excited about future centaurs.
I completely agree that breeding two creatures together with a ??? pairing and getting back one of the two parents feels bad. (The reason that you try out the ??? combinations is because you want to get something different, not what you started with)
Currently, the breeding master gives you a list of recipes you can make from creatures in your stable and your recipes, I think it would be great if he added creatures that you have cores for but haven’t summoned to the set of possible parents. (Perhaps mark with a * the cases where you are missing one or both parents in your stable, but you have the appropriate cores and could summon to make the breeding work)
Personally, I quite like the Heredity system. It seems like a natural and reasonable well-balanced way for breeding to increase the power-level of my creatures. More importantly, I find personally, that when my creatures reach max level is a very natural time for me to re-think my team. I find that the current system encourages experimentation with team composition. Typically, I will take my couple favorite creatures and breed them in a way that produces offspring identical to the pedigree, and for creatures that I am not sure about, I will breed them away to produce something else … sometimes I get something cool that I end up really liking, sometimes the new creature doesn’t work out especially well … but either way I enjoy the fun of trying out something new. (And in the case where the offspring is a high-heredity creature that I don’t end up likely a lot, I can always breed it again and try something else)