Its a specific trait of japanese genre fiction, its not even particularly unique to JRPGs which IMO are less overrun by hero's journey than they are coming of age stories. A good example would be the Yakuza games, starring a man who starts in his late 30s then eventually is near 50 by the end of his arc, Kiryu is every bit as naive and idealistic as your typical JRPG lead. I think it comes down to a larger focus on ideals as a story telling device, they are less interested in gritty details and minutia and more on bigger ideas that divide or lead people/groups. You point out the plucky heroes but just as common is the well meaning idealistic bad guy who believes what they are doing is for the better of all. I do not see this as a bad thing or even an annoying thing, its just a different perspective on plot and character..... the very good ones do more with it and develop beyond cookie cutter characters and tropes while the lesser games use it as a crutch. As others have pointed out the western style is just as trope heavy and filled with identical plots but just with different tropes they focus on, to me an idealistic romp for well meaning good in a jrpg is an antidote to the countless gruff cynical everyone and everything is fucked tales coming out of the west. They are different types of unrealistic, in the jrpg sense it is realistic that a person would believe those things and work towards them..... unrealistic that they would accomplish much with it; for the western ones its realistic that a world is not black and white and good doesnt always triumph.... but unrealistic that the violent cynics are or would be heroic in any way (I BELIEVE IN NOTHING BUT KILLING THE BAD GUYS).
Anyways its not counter to your criticism of JRPGs sharing a lot of DNA but a game series like the Falcom Trails series or the Suikoden games take those starting points of common tropes, then just go the extra miles developing the characters and situations into being far more complex and interesting. Suikoden with its plots of civil war and family, Trails with its intense focus on developing every character (even npcs) into being fully formed 3d characters. And honestly that is what tropes are for, they are a shorthand so that we can understand a character quickly and get up to speed, the good stuff builds off that. Tropes are not bad.
There are JRPGs that deviate from this stuff, but they are rarely the big budget mainstays. Absolutely never expect DQ to be anything but what it has always been, the series is great but its almost about being a comfortingly similar tale each time, FF is designed to market to the largest base possible. Try stuff more off the beaten path, SMT games are rarely about coming of age (outside persona), the tactics genre is usually not as well so try Tactics Ogre or Front Mission. Radiant Historia is a really overlooked DS (and recently re-released on 3DS) traditional time hopping jrpg starring an adult mercenary with loss issues. The Shadow Hearts games are really good too (getting kinda expensive though) in their strange setting and oddball characters. I would stay away from Tales of games, I enjoy them enough but they are jrpg/anime trope heaven and much of the enjoyment is getting to know the characters and seeing how they will slightly tweak expectations of those tropes game to game.