that missle locking room ( and a few others with similar objectives to get out ) aren't telegraphed well enough. maybe exclude all the light sources, and have one shine on the spot you're spposed to hit, or maybe have your suit tell you abnout it, point it out and act as a tutorial, so the player knows to keep an eye out fot things to shoot and reveal the paths.
other than that, this is fantastic - i can see the metroid influence, but it didn't feel like I was playing metroid - which is a good thing.