Let:
*cloning->keep the parents alive
*fusion-> kill parents
Just read this thread (that link there^), so the objectives of the the new breeding system is to emphasize specie rarity and control the inflation by stopping the cloning. So why not we pay to the daycare huge money to do the 'cloning', and the higher the 'rarity value' of a certain specie/group the more expensive we pay? Like cloning rattata costs $100,000 while cloning salamence costs $1,000,000. If a player can't afford the cloning then daycare resorts to 'fusion'. With this system, the player has the option to whether to clone, fuse or don't breed at all. This also preserves the rarity of species since the price of cloning differs. This also control the economy because huge money will go to daycare and also raises the price of rare pokemons.
It's like paying professional fee to the daycare for convincing our pokemons to have sex. If we can't afford the PF then our pokemons they do the 'fusion pose'.
To sum up, old/rich players becomes richer while new/poor players... do the catchMMO and catch up.