What I don't like about the new version of breeding is the requirements and how hands-off it is. It doesnt feel organic, you just shove the pokemon in and forget about them except to feed them random blocks (that are super inconvenient to find) and whatnot. The old system was really enjoyable because it rewarded you by telling a story, seeing the pokemon physically there was overall just super cute especially with the heart feature and the little text that told you they were falling in love. Having to create a whole environment for them made it enjoyable and unique, and gave reason for people to actually /build/ something within the game. Taking in account that this mod is literally minecraft, I think a breeding system that encourages the player to build something, such as a whole environment or maybe a whole center where they keep all their different pokemon, is much more rewarding, as opposed to just having it in a GUI.
Overall I just think that features that encourage more storytelling and physical should not be removed for the case of GUI's. I would love in the breeding system could be altered in some sort of way.