Oh, no worries, Ascovel! I'm not in defense mode. Just explaining my motivations!
The bottom line is that the game is supposed to be fun and I think solving a substitution cypher is a fun brain excercise. Like Sudoku. If it was a more complex cypher that required pencil and paper or, going the other direction, some cypher that just requires the player to type in a password, I'd be worried that it wouldn't be as fun. That's all.
Crimzon: All of it. Shane's herculean accomplishment of making all the fiddly animations I asked for in the game definitely took him a while! But the real bottleneck was scripting.
I can't even begin to estimate how many man hours it took. The first six months of the game were spent putting all the game systems and main GUIs together. The game does not use AGS's built in inventory or speech system. All of it was custom coded. After that, implementing each room would take a month or more because of all the different ways you can examine/interact/combine objects with all the different characters. I designed the game to be more complex than I ever should have.
Add on to that all the writing! Four different lines for examining each object in the game... (though we cheated sometimes) plus all the STMs. I was a fool to think this STM + 4 player characters was a good idea!
The best part of coding was doing all the little interactive or tactile sequences, like the maze or key/magnet or puzzle box. I loved programming those, they were so much fun. But they still took time. A week or two for each. So, when Janet was working on all that other boring stuff, I worked on these!

Finally, my personal life was responsible for significant slow downs. When I was the only programmer, I was working only after getting the wife and kids in bed. I'd stay up as late as I could function and then have to get up three or four hours later for work. That's why the game may have never gotten done without getting Janet on board!