Playtest much? Oh, it's supposed to be like that.
I thoroughly enjoyed your previous two entries in this series. This one, however, has some issues. For starters, the bat boss flew away from me and won't come back down. It seems he got "trapped" on the upper level, although I can't say for sure since I can't get up there to check. As a result, I felt like had to start over. Later on I discovered you aren't supposed to fight him until later, but it sure looked like you were supposed to drop bombs on the little blue gem on his head. It felt like I was supposed to kill that boss at that time, but since he flew away to the upper level and wouldn't come down, I just assumed that the game was bugged. I generally tend to stay away from games with problems like that, but luckily for you I'm a little more lenient considering you are an indie game developer and your previous two entries in this series are good.
Also, later on in the game, some of the moving pillars in the Processing Station got out of sync, which made it impossible to cross them without taking damage. Fortunately, thanks to the bubble, I was still able to make it through there to get another bomb upgrade.
I think the main issue is not being able to advance through places you are able to get to. In Super Metroid, you are able to pass through some places that you aren't "technically" supposed to be as long as you are skilled enough. When I came across the bat boss in your game, it felt like I was supposed to kill him at that time, but it took a short while to figure out otherwise. If the boss is out and about, one can only assume that you're supposed to fight him. Perhaps it's just level design, but I think you can do a better job of clarifying where the player should investigate next. I do prefer the non-linear approach, but it should be clear to the player which places are open.
The game mechanics, frame rate, and graphics are all great. Just work on the things I mentioned and the game will be a lot better.