Zach, the main flaw was the fact that the allies got hold of it before the war started. They had to keep it a secret and even let soldiers die so as not to give the Germans reason to believe they were hacked.
Here’s another system. Open a large bitmap picture in a byte editor and replace every twelfth bytes with the byte of your letter.
Or get the byte values of your message, multiply them by a predestined number, encode it in base64, then multiply again, encode in utf8, and so on.