Coming up with a story is the easiest part. Writing it for a game is the hard part. Majority of RPG Maker games get this horribly wrong with their 16 minute introduction cut-scenes with pages and pages of text to mash-through because the developer accidentally wrote a film script for their story that they spent more time on writing the origins of the universe than actually detailing the game-play experiences the player has.
Then the actual story is written so incredibly rigid and single-minded that the game turns into a top-down visual novel and does nothing to exploit the player's freedom and ability to make choices.