Let me walk you through how these choices really matter in gameplay. The main thing to understand is the timing of your decisions during key moments. When targets surrender or beg for mercy, you've got about 3-4 seconds to make your choice before allies like mitsumune might act on their own, which can lock you out of certain paths. During the stray dogs sequence for example, keeping those soldiers alive opens up yaya's questline almost immediately after the scene ends.

Combat-wise, sparing targets often leads to tougher follow-up encounters since those enemies tend to regroup with reinforcements about 2-3 minutes later. Important tip though - if you're going for a non-lethal approach, position yourself near wooden structures or hay carts since knocked-out bodies are way harder to hide than eliminated ones. When dealing with shinbakufu leaders specifically, watch for their guard patterns - they have a brief vulnerability window right after their power attacks where you can either finish them or apply a sleep dart.

For the best rewards and ally relationships, pay attention to your positioning during key decisions. Stay within 5 meters of potential allies when making moral choices, as this affects their reaction timing and dialogue triggers. The game tracks these moments pretty carefully even if it's not obvious at first, and while the main story doesn't change drastically your options for stealth approaches and companion support definitely do. Keeping targets alive might make individual missions trickier but having more allies for those tough shinbakufu fortress raids later makes it worth considering.