Something that I was asked a lot or that I see you have missed is the use of the Prodigal Compass.

The place where it´s most useful at the beginning (following the plot) is in the forest.

Legend has it that the Lux morteM forest has no way out, and in fact several players have experienced it!

But, you are supposed to have the prodigal's compass with you, you just need to equip it.

Now notice that where the backpack (the inventory) was, the icon has changed to the exit door.

By clicking on it, you will be taken to the forest entrance again.

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In the following video (although in Spanish,  and the quality of the video is bad!) you can see how the characters react to the items, this is very important! as it is part of the mechanics, is not exactly considered a "puzzle" as it is quite basic, but, there were people who got stuck in the part of the queen ysdra or when Komodo asks for a test, although the dialogues give you clues, I think it´s also because they did not understand the mechanics well.

Also, know that in the VN, you have "a lot extra content" aside from the main quest, either by chatting with the characters, experimenting with the items and their reactions, or using the items in other places, you can discover various secrets or details of the lore and history of the island and its inhabitants!