With each difficulty, since (typically) the save point frequency and locations are the only things that change between difficulty, you need to strike a good balance. So far, there are a couple parts that I think are out of whack.
I haven't yet taken the time to actually go through each area and determine which save points should go where. Most of the placements for them so far are simply a hunch and then I move on to something else. I'm still working on that.
Boss fight:
Awesome fight! Considering you don't have a gun yet, this is a fun fight! It was a bit easy on Pansy. Do you give the boss more HP for the higher difficulty levels? I would suggest it. It was OK for Pansy, but he's too easy for even Medium.
So far the difficulty has no impact on anything but the number of save points. However, I do agree that giving the boss more health on a harder difficulty would be a good idea.
...and yes, it is from Blaster Master

Good call
It seems you've seen just about all there is to see for now. The details are in the works, such as save point distribution and things like that.
Thank you for your awesome compliments! They are very encouraging! This project will be taking some time, as I really am a bit of a perfectionist with things and I want this to be a very well-rounded, well polished game.
As far as the 'metroid-vania' system and presenting the player with annoying dead ends... I thought about that for a while. I thought about metroid, which is full of dead ends, yet it's a loved classic. The difference there is that the halls of the Metroid were reasonably easy, especially compared to a game like this, which is full of ridiculous traps and deadly obstacles. You are right about it being a challenge getting the balance right. You want to allow enough exploration to make the game not-so-linear, but not so much exploration that the player ends up spending 2 hours and 500 deaths just to find out he's at a dead end.
Obtainable abilities, I think, is another really fun way to add a bit of anticipation to the gameplay. The levels and zones of my game will be specifically designed so that they can each be revisited later on, and having those extra powerups will allow you to access additional areas in those levels you couldn't reach before, such as secret item rooms and so on. I am aiming for a high replay value in this game.
Thanks again for your encouraging feedback!
PS: Please be patient with the whole "uploading new builds" thing I have going on. I'm trying to find an effective way to share the builds on various sites easily, and I'm currently also trying to see if I can efficiently track the number of downloads they get from each, which is why you now might see the "download count" counter on the original post. I may change my mind on how to go about things quite frequently, so please be patient with my indecisiveness there.