This was great! Like Armageddon said, the fading and sound worked really well to create the atmosphere.
Spoiler
I especially liked how the ending makes you think of the aliens differently if you play through a second time (the first time I just assumed they were scary and wanted to eat me, the second time I wondered if they were benevolent). I guess it's similar to what Cogliostro was saying about reinterpreting the commander on the second go. I had the same problem as everyone else with solving the door puzzle the "good" way but finding out the answer from this thread for my second runthrough didn't detract from my enjoyment.
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