Free roaming non linear Jrpgs do exist.
It's just that most of them have not been translated into English.
The meager few that came to the West are already mentioned in this thread.
(Metal Max)
The problem here is that most Western Jrpg fans usually can't stand Jrpgs that differ from the norm. (The adventure game/movie hybrids.)
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Here's a couple that I've played or owned.
Sword World & Sword World 2 for the Super Famicom: These games were based off of some Japanese D&D pen & paper knock off.
It's one of those games where you get to create your entire party & then get to explore the world around you.
While taking a couple of side jobs/side quests in between.
Hell I still have no idea what the hell the main quest was.
ZIll O'll & ZIll O'll infinite, Chaos World, Wizap,Dark Law, are some of the others that come to mind.
Taiko Risshiden V: Possibly the most open ended Japanese game that I've played.
I'm not even sure if it's considered an rpg by Japanese standards
This game is set in Japan during the sengoku jidai. It's one of the few console games I've seen where the game world reacts to your every action.
Your choices constantly affect the consequences of your character's every move.
In one game I was fired from the job, because I couldn't understand what the hell I was supposed to do, but it didn't matter.
I later ran into a girl (Nene, Hideyoshi's real life wife. I was playing as Hideyoshi.)
who was getting jumped by bandits.
I saved her & then she married me.
I then went around the entire country of Japan just mugging everybody I saw so I could sustain somewhat livable conditions for my wife.
I wanted to join the various ninja clans that offered me protection, but I didn't want to risk having them hunt me down in case I failed one of their tasks.
(Due to not being able to read wtf is going on in this game.
Even some Japanese natives have problems trying to read Koei strategy/rpg games, because of the advanced kanji that's used in the game.)
My game finally ended when I tried to jump a samurai.
Only to see him one hit kill my guy when he threw a big ass fireball at me.
(Which is surprising, because Taiko Risshiden is a mostly realistic game. Or at least it was until that fucka burned my ass up with his animu fireball.)
Note: You're supposed to try to unify Japan inTaiko Risshi den, but this is just one example of how open ended Taiko Risshiden series are.
You can make a living as a pirate, a gambler, warlord, a dancer, etc.
These games are very similar to Uncharted Waters.
Which is no surprise, because both of these games are created by the same guy.
Romance of the Three Kingdoms VIII, & X: They're supposedly strategy games, but they feel more like bbs based text like rpgs.
You can start out as a merc, and eventually build yourself up to become the emperor of China.
I might try Tactics:Ogre or Romancing SaGa: Minstrel song, but judging what I read about them I don't have much hope I will enjoy it.
If by Tactic Ogre you mean "Let us Cling together", then yeah you need to try that game out.
It's one of the only tactical Jrpgs I played that actually had depth, and the plot for the game is far better than most of the tripe that I see coming from console games.
Minstrel Song is actually one of the only decent rpgs on the PS2, but it's mostly for the random ass battle system, the sountrack & the exploration.
However I'd much rather stick with the likes of Arcanum when it comes to non linear rpgs in general.
(minstrel song had no C&C, shit dialogue,& story.)