The crux of the issue is that puppies from puppy mills (and even private breeders) are often bred beyond the levels that are needed to sustain demand for those particular breeds. The problem with this is that eventually the unwanted animals are euthanized.
It's an easily preventable problem if people follow Bob Barker's advice and spay/neuter their pets, and if more folks choose to adopt pets from shelters/rescues. Obama has a nice opportunity here to set a good example, but ultimately, it's his decision.