What I see in the original post partly comes out of the focus of JRPGs vs WRPGs:
* In JRPGs, you have a detailed and forced narrative the game designer wants you to go through. There is focus on preset characters with set backgrounds, and a plot that needs to unfold. Side quests provide a way to level up so you can get to the ending. Because of this approach, it is possible the main story arch isn't going to be completely revealed. It will eventually be reached, because the forced narrative will get you there.
* WRPGs, on the other hand, are all about choices players make, and the characters are who the players decide they will be. In short, it is YOU who the game is about, not some other character you are following. A game is likely to give the player multiple possible endings. The game world functions much more as a sandbox than the JRPG world. To prevent players from getting completely lost, the game will put some long-term goals for the player to accomplish and lay out more of where they need to go. The basic state of the world is laid out also, to give players an overarching focus, so they stay on task, and get to the ending. This is needed, because there isn't a forced narrative placed over the game.
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