Primates are a great strength of both zoos. I was at Frankfurt Zoo this summer and the Great Ape House there is superb, with indoor enclosures that are perhaps the best I've ever seen in my lifetime of visiting 520 different zoos and aquariums. However, while the outdoor Lowland Gorilla and Sumatran Orangutan exhibits are decent, the outdoor Bonobo yards (with around 16 of the apes) are not up to the high standard of the other great ape habitats.
Even though the Borgori-Wald in Frankfurt is superb, the Small Monkey House is destined for the bulldozer as it's seen better days. It opened in 1962 and although the primates probably don't care, aesthetically it is very poor. There is also a Hamadryas Baboon mock-rock 'blob' that is awful. Frankfurt does have a nice gibbon island and some primates in the iconic Grzimek House that are all in very good exhibits.
While Frankfurt is arguably one of the better zoos in Europe for primates, mainly due to the presence of the Great Ape House, San Diego Zoo is superb for primates. The Lowland Gorilla, Sumatran Orangutan and Bonobo exhibits are all top-notch, although there is no indoor viewing of the apes. Yes, there are Aye-ayes in horrendous corn-crib cages and it boggles my mind that a zoo as famous as San Diego still has such outdated accommodation. However, it is important to note that in locations such as Africa Rocks and Lost Forest there are world-class primate exhibits around every corner. Large, netted exhibits with lots of climbing opportunities are the norm and San Diego is probably, off the top of my head, the best zoo in North America for primates and with at least 25 species on-show. Frankfurt does well in this category, but it cannot top San Diego. I will say that I don't see how this can be a 3-0 victory for either zoo...that would be a harsh assessment.
I'm voting 2-1 San Diego Zoo
P.S. When all of these ZooChat World Cup groups were announced, I originally declared that Group D was the 'Group of Death' and I stand by that statement. Even if, hypothetically, San Diego and Beauval advance, I feel bad for Saint Louis and Frankfurt...two really fantastic zoos.