I haven't visited Zoo Aquarium de Madrid, but both Faunia and BCN are great zoos. Faunia centers around more "rare" species and in "zooinmersion" in some exhibits, with animals like Eastern quolls, the only manatees in Spain, Steller's sea lions, Gray brocket (only ones in Europe), Aardvarks, a great collection of penguins,...
Barcelona has also some really cool species, but exhibit cuality is in general way worse than in Faunia, since it's a old zoo now renovating. Barcelona has one of the (if not the best) best Reptile house in Spain, Black-faced impalas, Libyan barbary sheep, Mhorr gazelles, Monstey brook newts, a great bird collection,... Also, if you are not familiar with Iberian fauna, BCN has you covered! With Iberian wolf, Bearded vultures, Griffon vultures, Egyptian vultures, Mouflons, Local species like hedgehogs,... (If you came some years earlier, you could have seen Spanish ibex and Spanish red deer, no longer in the zoo tho).
In conclusion, I recomend both zoos.