I just played through this, and it's quite an enjoyable Zelda-like experience. I'm a big Zelda fan, and as much as I love the 3D games, I do miss some of the more straightforward 2D experiences. I managed to find everything in the game except for one heart piece and one gear (and the reward for finding all of the gears).
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That was a very informative read. Thank you for sharing. Even with the difficulties you mentioned, the game is tightly designed and extremely well fleshed out for something created under such strict time constraints.
A couple of thoughts on the accessibility issues you mentioned... A bit of text or auto-opening the map could help to explain where to get your suit when you die. Communicating the room clearing aspect could be done by locking the player in a room with enemies once or twice and not letting him leave until they are destroyed. Even those first two scientist-zombies could block your path back to the cloning chamber when you return with the suit.
Regarding the ending, it's a great concept, and I think it's totally worth being obtuse about what the player needs to do and where he needs to go, especially since it fits so well with the theme of the game. One way you might make this more obvious without hitting the player over the head is to more clearly communicate that the docked ship is just that - a docked ship - and not another part of the station. A computer terminal outside the door could help to explain this overtly, or you could have the player run through a long docking tube before reaching the ship, which would make it stand out from the rest of the experience.
Anyway, just a couple of thoughts should you decide to revisit the game. It's absolutely worth playing as it is, and the accessibility issues actually play into the game's charm, its sense of dread, and the overall feeling that the odds are stacked against you. It's funny that the recharging stations didn't work out in the end, because this only helps to further support these themes.