I love this concept, and you've done a lot of fun things with the game. I would never have imagined this type of mash-up working, but you've pulled it off very well. The atmosphere is perfect and really makes you feel like you're exploring a Metroid game. I agree that the RNG can feel a little unfair, but there's so little consequence to it as long as you save that it hardly matters.
The only real gripe I have is that maybe you could involve a little more choice in it. It's terribly linear as it stands, and there's no reason to give it another go once you've played it. Other than that, you've done the most important thing, which is left me wanting more. ;)