If you're willing to check out non-RPGs, then I highly recommend Star Tropics (which is on the flowchart). The best way to describe it as a cross between MOTHER (setting) and The Legend of Zelda (gameplay). An interesting thing to note is that Star Tropics is a first-party Nintendo game that's never been released in Japan despite being developed there.
Another thing is that there's a point where you'll need to get a password off of the Internet. The game originally came with a letter from the protagonist's uncle that contained the password, which would only be revealed by dipping the letter in water.