Well, I understand the sentiment of people who say "Giving you options is pointless if it doesn't actually affect anything." I enjoy different options just for the sake of seeing the varying reactions, but I do understand people who want to see their options actually have a lasting impact on the story. I just don't think picking "bad options" necessarily sabotages the story, but not everyone will see that my way.
I do agree that there's likely a "canon" choice for some of these major decisions, but unless Square actually tells us what they are, it's mostly speculation.
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