Sacrificing two Pokemon to get one is already strange, and doesn't suit Pokemon's world, story, themes, etc for a lot of people. It's detrimental and unapproachable to various types of play that isn't cold, stat-driven, competitive play, and likely isn't necessary for the competitive side of things either.
I say likely, because perhaps I'm missing something, but so far it seems the main concern it addressed was trying to prevent an overflow of high-powered Pokemon in the Global Market.
If that's the biggest concern it addresses, why not just make bred Pokemon untradeable and unsellable? This would keep the global market from becoming saturated, and make it so those who want bred Pokemon can't just buy a piece of the process, or a battle-ready Pokemon. They have to grind it themselves with what they've caught themselves, and works well for an MMO. People who want to breed for competitive can do so without other players having to sacrifice their Pokemon just for an interesting move they wouldn't otherwise get. It also lets the more RP heavy players do things without grinding in an unsatisfying, uncomfortable, or depressing way. Additionally, players won't think they can breed Pokemon only to find out they can't (as they have to choose between their hard-earned Pokemon and a baby they've never used in battle yet), or that the process just isn't worth it.