It is difficult to incorporate abstract choice and consequence and have the intention of the designer be intuitively understood by the player. Through the Darkest of Times does a pretty good job of distilling abstract ideas into gamified patterns that the player can learn. This game does have the foundations of that, and the fact that I am comparing it to Through the Darkest of Times is a compliment. I guess the design question you should ask is 'how can the player systematically make decisions with clear intentions'. Good job!
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Yeah, that's the biggest issue we had designing it, how to give the player control without making the game all to easy. Overall we decided to lean more towards the easy side because at least the full story would be able to be experienced that way. If we had the time we would absolutely be spending more time on balancing and tweaking how the various changes are actually communicated to the player.