It'd be a more interesting debate if we looked at the theories and practises behind both academies and compared their success rates since Cruyff's revolution. Both academies aren't afraid from scouting and inviting/buying/whatever youngsters but that is seemingly where similarities end. Besides, football is observably a sport of cycles, it can be seen in tactics, style, formations, positions, and personalities. For instance in the early 90s Barca had: Guardiola, Ferrer, and Busquets (that I know of), a few years later Real had: Raul, Guti, and Casillas. Barcelona came back with Xavi, Puyol, Iniesta, and Valdes, while Real floundered about and let players like Arbeloa, Mata, and Negredo leave, the Barcelona turned up the heat with Messi, Busquets 2.0, Pedro, Pique, and Alba. Of course it returns back to Real with Carvajal, Nacho, and a few others on the wings.
Castilla isn't bad by any stretch of the imagination, but it's hard to argue that La Maisa isn't the modern standard. The only academy that could give La Maisa a run for it's money is Ajax's.