This is tough because really this is like comparing apples to oranges. The FCI is an organization with very different goals than the AKC.
Because FCI rules and regulations are designed to improve individual breeds and to safeguard them from exploitation by humans, its standards often read very differently from the AKC which have no such rules or regulations. The AKC is not about "quality" at all in dogs, it is a sports registry only and a multiple breeds registry. The FCI however provides single breed registries, focusing on each breed.
Although the FCI is not perfect, if you can find a reputable breeder that adheres to the FCI, this would be your optimal choice. Please keep in mind however that breeding standards and FCI adherence resides with each member country - so as you would expect, some countries have better standards and safeguards than others. For example, Switzerland and Germany have poor standards whereas the scandinavian countries have great standards for breeders.