Didn't read OP but I did read the part where you said puzzles should DEFINE Destiny, and I don't think that's a good idea.
Puzzles in the game, sure but not make it a puzzle game. If you mean like Dark Souls where the game just throws you into the world and you have to figure out what to do on your own then sure, that's not too bad, or learning about the game through context clues or item descriptions, eh I wouldn't mind that too much, but making it full of pure puzzles when I just want to shoot stuff is not a good idea either.
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The title makes more sense in the context of OP. The intent was to indicate that mysteries/puzzles would be a defining element that distinguishes it from other FPS/RPG hybrids, but I was not saying it should be the only element or a major one one in terms of frequency. After reading your thoughts, I feel you are closely aligned with what I would like to see.