Really, the only JPRG I ever played was Sweet Home (one the firsts survival horror), even because seeing my friends playing them I felt them as "guided adventures" than real RPG, but I can list many Japanese works starting with good ideas but at end they drift to non-sense.
Anime: Sousei no Aquarion, Dragonaut - The Resonance, Elven Lied, and the world famous Neon Genesis Evangelion (I hope the new remakes will bring a new, consistent ending without too much free abnormal psychology).
Movies: Suicide Circle (strong message, but boring movie), Loft, Ring 2, Ghost System.
I can't say if the "limits" I spoke about are really in the lack of abilities of the new designer/writers or in the commercial needs of the companies they work for. I want to believe in the second option