Thank you very much!!! I'm glad you enjoyed it that much, and I appreciate the review too ^^
To adress some of your concerns:
Story: There are reasons for all of this of course! I can't get into it, but things will be explained eventually ^^
Gameplay: First of all, there definintely needs to be balance improvements. Too much is introduced at once currently, I want to make things more forgiving from the forest onward. This is where the WIP status shows the most...! Other planned changes will also help with this. I'm surprised that the gear puzzle gave you more trouble than the color ones actually! But it's true that that last one is especially tough, I've heard similar things from others. Noted! Some of the secrets are a bit too well hidden, though characters being sad isn't a secret indication, just a little mechanic where you can tickle them to get some shards and sometimes items ^^
I plan on adding some form of secret detection unlockable later in the game, so you'll be able to get anything you missed eventually. Possibly along the lines of what you suggested, but I'm not 100% sure yet!
when it comes to the BE, I agree! I'll actually redirect you to the FAQ since I have a good answer for this there: https://www.patreon.com/nosebecc/posts/faq-walkthrough-119207938
I have plans, and the next major update will be called the BE update, focusing on (but not limited to) fixing this issue.
Again, thank you very much! ^^