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Allow me to address this: "The problem is that speedruns can drastically shorten a game's length, which is especially bad in story focused games and lore focused games like mine."

While I cannot speak for the Fan Favorite award, for the Top Three places, the judges will each judge based on their own criteria. Therefore, if your game is heavy-story, some judges will focus more on that, while others may focus more on gameplay, and others may focus more on aesthetic. Getting the four judges that we did (each who are experts in different aspects of Game Development) was on purpose. That way, each game gets different viewpoints before it moves up or down in the ranks, instead of just relying on one thing (like a story-focused judge playing a game with little story, etc.)