Warning: sorry if this post comes out a little scattered. I'm just making this up as I type.
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Walking through the cold today, I revisited the idea that had struck me before: a Minecraft RPG, based mainly on the first hours of the game (ie. when you wake up on the shore, with no resources and start building and exploring - not the late game where you're building ziggurats and impossible towers). So, obviously, the first thing that I considered was the system. I started designing something from scratch, but then I thought why not look at existing games.
So, oD&D comes to mind, Apocalypse World, a bunch of other stuff. But I think Mouse Guard really stands out in many ways. The man (or mouse) vs. the vast wild theme, the craft and trade skills, it's all there.
Now, the turn structure should be loosened up a bit. My first impulse is to model the GM turn-Player turn structure on the Day-Night cycle in MineCraft. At night, the monsters come out, during the day you rest and build. There's a small, but not insurmountable problem with that. Nights in MineCraft are largely passive, as you lay down in your shelter, whereas in MG, the GM turn is much more active...but it can work.
Beliefs should probably also be handled a little more liberally than the book suggests. Maybe.
I'd look at my documents where I deconstructed the Recruitment procedure and make it a little more straightforward.
For Resources...I'd have players start out at 0. Foraging the remains of your ship and collecting resources on the island would give you dice at hand, not unlike BW.
Circles...now this can be a problem. My first idea is to make it a sort of Flashback check (influenced by Lost).