From what I saw, it appears that the "tradeoff" for getting rid of the hybrid islands was also getting rid of some of the more generic islands (the ones Ninji referred to as Island 0, Island 1, Spiral Island, and Fidget Spinner Island).
I guess their logic may have been that we all have Leif now so we can breed whatever we want, whenever we want. Also some hybrid islands (hyacinth, windflower, rose, mum) were better than others (cosmos, tulip). As someone with native cosmoses and sister flower tulips, I had all of the colors for each of them before I found my first hybrid island. It's really annoying that they just got rid of a bunch of islands and made the remaining generic islands more common instead of adding new ones.