jRPGs have...well, they have very japanese attitudes. For example.
Video games, along with anime and manga, are sold in Japan primarily as escapism. For that reason they tend to be more cinematic. The idea is that you submit yourself to the story and enjoy the ride, not worrying too much about making choices or challenging yourself. Western RPGs, on the other hand, tend to be open-ended, free-roaming and place the emphasis on the decisions of the player. Compare a game like Final Fantasy, where your choices are limited to your stats and a few dialogue options, to a game like Oblivion, where there is hardly any story and the gameplay comes from exploring the world and interacting with the world in the way you desire.
jRPGs are comfortably not interested in originality. In a japanese game it is considered better to tell a story that has already been told (or to refine it and tell it again) than create a new one. The infamous cliches of jRPGs are intentional. They're familiar, they're safe, they sell. Western games, on the other hand, while filled with derivatives, consider originality a prize. You're more likely to see a new story from them.
Since marketability is so much more important in jRPGs, fan service is seen more often. You're more likely to run into big-breasted catgirls, dominatrixes, engage in a lesbian rub-down mini-game or encounter incest, homosexuality and pedophilia. Western games are rarely devoid of fan service, but they do have less stylized kink and it is more likely to run into a game that sacrifices the marketability for a more believable game, or one with more integrity.
And finally, perhaps the biggest difference of all: Cultural themes. jRPGs are loaded, brimming, overflowing with pro-japanese cultural themes. See if you've seen these before:
A) The group is stronger than the individual. Aka, The Power of Friendship lesson. The party bands together at the end to conquer the villain, or the hero is unable to overcome his problems on his own until his friends rescue him with the power of not being alone.
B) Youth Worship. For some reason you have an irresistably adorable child in your party. She might be wearing skimpy clothing. Everyone in your party is 17 or under except the "old man," who is 32.
C) The ideal woman (your love interest) is timid, soft-spoken, child-like, virtuous and ready to sacrifice herself. She apologizes profusely and often.
D) Nature is sacred and powerful but is under constant threat from mankind. However, it always wins in the end.
E) A technologically advanced country attacks and invades a peaceful, nature loving country. One jRPG went so far as to have the kingdoms known as the "western kingdom" and "eastern kingdom," respectively. Yikes!
F) The destruction of a Christian-like religion.
These are all jRPG cliches that would never show up in a wRPG but are present in every jRPG because they reflect values of that society.
