The goal is to incentivize legitimate pokemon.
They know that every professional player hacks their pokemon in, so they're simply turning into the skid and removing the hastle of IV breeding and EV training. They're also making competitive shiny and legendary pokemon exponentially more available.
And at the end of the day, unless you started competitive play this year, it only takes about ~15-20 eggs before you get your perfect egg, so it's not a big deal.
There's also the fact that the next season of VGC is likely going to limit the selection to the Alola dex, meaning you will have to re-breed and re-train all of your pokemon anyway, and this system will save that time.