I don't know how it is in that game xD
Here the secondary stories will add a lot of depth to the lore, details that otherwise would not be possible to know and many new possibilities too :)
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I don't mean that sercondary stories are bad at all, don't get me wrong. Especially in a game like yours which is, let's say, sandbox-like, it is good to add a lot to it. And yes, I know about that aspect of adding more details and info on the story, Kaede herself is evidence of it but my fear is stated above.
But I trust your script and I'm eager to know more about the story nonetheless.