Its hard to explain, I am no Japanophile but I will think they make the best games, perhaps its the subtleties, their style? Flair? something.
I just cant see an american or european dev making a game like MGR as cool as they do it, maybe cause they dont care about being weird, wacky and awesome at the same time?
I dont know what it is exactly but when you play a game like the Souls series it distinctly feels Japanese even though it has a western rpg type environment/art style.
And yes I know not everyone loves Japanese games (I think some just hate to be different or because they get tired of hearing about Japanese games) but I think every hardcore gamer can tell when a game is Japanese or Western, and I dont mean something obvious like some anime cliché but something like the souls series, I think any hardcore game can pick up the souls games without knowing anything about it and come to the conclusion that its Japanese rather than a western made game just by playing it.