What a pleasant surprise!
I love pixel art, I loved Metroid, and these things practically ooze out of the walls here. At the same time, it's definitely -not- Metroid. I found myself wanting to collect powerups or health/ammo upgrades, but there are no guns and there are no powerups. Getting further into the game requires careful timing and coordination, as well as a good eye for puzzles. I enjoyed the fact that it was hard but not -too- hard.
If you seem to notice that the game is glitching out, it is not. My experience is that there are no bugs in this game, and the controls work beautifully. Maybe what you're experiencing is intended behavior? X)
Actually, the glitching is the real reason I kept playing, and because of that I felt a little unsatisfied. There's no satisfying "CLINK" when you fit a gem back into your ship. There are no powerups to collect. The story is indistinct, leaving a lot to the player's imagination. This could have been great but the end left a bit -too- much to the imagination. I would have loved to know the fate of the planet, or the astronaut, or get a sense that something was accomplished by getting the extra gems. Even through all that, the game is extremely fun. Good work!