Are you saying that you've read books in general, or books specific to writing stories or story structure? The latter, while often dry, will help you in designing a story that people will like, just as you liked Treasure Island. If you feel that you aren't getting that from novels I understand, but it's very hard to extract that knowledge directly.

You can write the story however you want, story boards are fine for demonstrating your concepts and laying out scenes. However, for actually nailing down the specifics of the story you'll probably want something more like a movie script. The book (sorry to recommend another book to you) Swords and Circuitry has some examples of this style that you could use. If you're talking about a story for us here to look at, bear in mind that you aren't going to be able to post the whole thing here. You've already given us a good overview, a lot of the quality left to demonstrate is only going to show in the execution.

Thanks. I wonder if this mechanic can be possible in game maker?

Eh? Of course it's possible. Not that the design has pretty much anything to do with how you go about making the game.

So yeah. Your proposed mechanic would work in pretty much every development tool known to man -- including GM. Hmm. That makes me curious, wonder if this would work in RPGMaker? Never checked it out much so perhaps it doesn't support anything but vertical leveling?