This was easy for me, as I've actually studied cryptography. However, it was still clever and refreshing -- especially how some of the puzzles require the player to go "outside the box" -- and the puzzles worked well with the computerized theme. On the whole, it was enjoyable and satisfying, and the music complemented the atmosphere quite well.
Other than the issue with the riddle (which you mentioned in your news post) the only real gripe I have is that it's hard to tell where the message starts and stops on the "cries of truth" level. While this isn't a major issue -- the player can of course cycle through all the possible sequences of numbers -- I at least had to redo it a few times because I didn't realize that's what I had wrong.
As for the secret ending, it was of course brilliant. The hangup I had with it is that I thought the puzzle was related to the story somehow, as in the last game; so even after I solved it, I didn't realize what I had was the answer. I don't expect there's a lot you can do about this, though.
Regardless of all, this was excellent, and I eagerly await more of your work.