First step: you're obviously right, I add for example the Académie MimoSifcom as ASEC Mimosas' academy. I can't add CFDFA as academy of Africa Sports d'Abidjan, another example, if it's not in real life.
Second step: I set reputations for each clubs (in my database) every year. Concerned PA ratings for second levels, as I said above, the facilities are poor. It's not a question of researchers, quality players grew up in academies, in Ivory Coast there a lot of academies. How many players results in Europe from Songon FC, RFC Yamoussoukro or US Fermiers?, Zero. When a club have a decent academy I set it in the database as obvious (maybe I can forgot one or two, but surely will be in next game patch and so on).
As always if you have some suggestion with proof (facilities images, articles etc. Or club "X" have low quality facilities compared to reality) I'll happy to add into the db .