@kadakithis: I will make sure to carefully explain in the game and yes, I will provide means to take systematic notes as puzzles become larger and more complex.
@OhHaiMe: I really love Layton as well but as I said before, after what... 3-4 Layton games? The puzzles ate getting a bit recycled. With some 100 puzzles per game, everything has been done. Maybe if I REALLY put my mind to it I could come up with two, maybe three interesting puzzles but no more.
I really like my logic gate thing because on a story level, it really meshes well with the game I am writing. The puzzles are planned to get more complex the deeper in the codex you go. As for difficulty levels, how about this:
-VN mode: no puzzles, ever.
-Normal mode: you can skip a puzzle if you like.
-Puzzle mode: puzzle are not skippable.
Difficulty levels do not change the difficulty of puzzles, just the possibility of skipping them.
As for decryption, I don't know yet. So far I only plan one that would unlock juicy bits of background story but it is SIGNIFICANTLY harder than the logic gates, I could put a few more, easier ones but I don't personally feel they would be very fun.
@Franka: I am at loss here. The puzzles clearly appeal to my geek side but as a writer, I also have an artistic side that empathises with you. I'd be open to an option of more visual type puzzles as well because you're probably not the only person with such preference. The player could be offered to pick either the visual type or the logic gates. However, I have no idea where to start and whatever I come up with, it needs to be relatively painless to code since Jack has enough work as it is.
Match 3D shapes? Match complex 2D shapes to emulate a sort of "find the proper gate?
https://www.google.ca/search?q=idea+for+visual+puzzle&espv=2&biw=1680&bih=925&source=lnms&tbm=isch&sa=X&ved=0ahUKEwif2YDOgcDKAhWGOj4KHWlgDlgQ_AUIBigB#tbm=isch&q=tangram sort of puzzle with a computer flavor behind?
Throw your ideas at me people, my body is ready.