Metroid has always been a story for context game. Meaning the story exists solely to supply a reason for the events to be happening. Why Samus is on the planet and what she needs to do there is explained by the story. The story itself is not for entertainment, that's what the game is for. I think what Malstrom is worried about is that Sakamoto doesn't realise this.
"Now, a fun game should always be easy to understand - you should be able to take one look at it and know what you have to do straight away. It should be so well constructed that you can tell at a glance what your goal is and, even if you don’t succeed, you’ll blame yourself rather than the game. Moreover, the people standing around watching the game have also got to be able to enjoy it." - Shiggy
