In some cases its merely that the english voice acting is so terrible and without effort that the JP VA are preferred. If the English VA's are putting at least some real effort into voicing the characters, i'll prefer them usually since i don't speak japanese. Many dubbed roles for games early on, had TERRIBLE voice actors or barely passable which made the JP VA preferred. The emotions displayed don't require a mastery of the language to understand either, i.e. crying scenes.
This is true. With the Japanese ones, the vocational schools for it means that if someone at least passed the classes, there's at least a floor to how bad the quality can go.
That being said... square has had a really good track record for voice acting overall. From final fantasy, down to kingdom hearts.
I know I don't have complaints about the English speaking voice actors used by SE, but I also know I've heard people complain about Vanille, Hope, Rikku and Tidus with the FF franchise in particular.