When AKC instituted their Frequently Used Sires program which requires dogs that produce a certain number of litters to have a DNA number, a large number of alternate registries cropped up. I had never heard of ACA before I saw it in the ad and I went and did an internet search.
AKC is not perfect but it does offer breeders some options for providing more than just a piece of paper with a pedigree. I have gotten all of my dogs DNA'd and both the stud dogs I have used have been DNA'd so if a puppy buyer chose to, they could get a DNA pedigree. AKC also requires permanent identification of the dog in order for health tests to be listed on registration papers.
It is still ultimately the buyers responsibility to make sure a breeder is taking steps to breed responsibly. That means becoming educated on the diseases in the breed and the tests currently used to detect those diseases. Also, learning about the registries, titles, etc.
One of the main reasons small operation breeders don't use AKC dogs is because a breeder sold them a dog under an AKC limited registration, meaning the dog wasn't intended to be breeding stock, and the breeder intended for the puppy to be neutered when it was old enough. Sometimes people decide they are not going to get the puppy fixed, and will use it for breeding…at that point, any puppies produced from that dog are not registerable with the AKC. But the other registeries will sign those dogs up with no questions asked.