Give people power, and they tend to abuse it as much as possible. This is a pretty decent explanation as to why Breeding has gotten so restricted. I am going to give a quick rundown of the history of breeding as a whole. Forgive me if my information is either somewhat incorrect, or opinionated.
-Originally, breeding started off with "put two pokemon in daycare, get 5 eggs and bike until they all hatched" and this led to a large amount of abuse, as you could literally hatch 5 pokemon.
-Then they tweaked it. I want to say the first tweak was making it to where you could only have one egg, but the bike system was still in place. This was still abused.
-Then they tweaked it again. I want to say the second tweak added the "flags" system, which met with such GOOD response (not really). Moves counted as individual flags, so this could be abused.
-Then they tweaked it AGAIN, going back to the first tweak, but I think they removed the bike requirement and replaced it with actual time. This could also still be abused.
-Then they tweaked it for a fourth time, and I think this is the one we are currently at. This can't be abused as heavily as the previous four breeding mechanics, because you can't pick and choose as easily as you could with the previous.
They finally hit the problem on the head, which is the parent sacrificing part of it. Since you can't keep the parents, you can't breed then shuffle them around until you got the desired result.
I didn't really care for breeding, even back then, as I was, and still am a big CatchMMO player.
Still, I wished I had taken advantage of the last system and bred a watt-ton of Feebas.