Actually the story problems came from the Nintendo side of development. The original co-creator of the Metroid series wrote the story only with Japanese audiences in mind, in particular using the canon Metroid manga that only came out in Japan for references on Samus' character (like how she suffers from PTSD). Problem is these did not translate well for American audiences, since not only did we never get the Metroid manga in an official manner (we only got fan translations), but cultural differences regarding how Samus addressed her former military superiors that make sense to the Japanese didn't translate to non-Japanese audiences who expected Samus to act differently to the whole "taking orders" aspect.

It's also worth noting Team Ninja wanted to include more control options instead of just "Wii remote held NES style only," but the same co-creator vetoed that idea. Granted I got used to the controls, but I knew having an option for Wii Remote+nunchuck would have helped out with stuff like the first person missile firing.

You are supossed to hit he mouth when it opens.
To get it to open you have to hit the balls… What?