I see The Great Cipher is synonymous to the simple monoalphabetic substitution cipher, just on steroids. The concept is the same—one cipher letter or multiple cipher numbers represent a number of plaintext letters. However, what makes the two so different in their difficulty to be cracked lies in the sheer possibility of combinations that could be created from each cipher.
The cipher key was not limited to just one letter replacing another; instead, a few numbers represented syllables. Thus, this opened up a lot more possibilities to stump cryptanalysts.
Before, it was clear in monoalphabetic substitutions that one cipher letter represented one letter of the plaintext. Therefore, we were only faced with a certain amount of different cipher keys to deal with. Even though a completely random monoalphabetic cipher would yield so many possibilities, frequency analysis could easily help decipher it. But now with a cipher with undeterminable characteristics (does "1" represent a letter or does "123" represent one letter? Or a syllable? I'm guessing they did not know how many numbers represented how many letters), patterns that lead to the cracking The Great Cipher become less obvious. There is a multitude of syllables that exist in the French language, making combinations all the greater in amount. This increases the difficulty because although we might see a string of numbers or other patterns, the specific plaintext it refers to—whether it be just one letter or two or three—has much more holes and traps.
In addition, many people might still be familiar with only the mono alphabetic substitution (since cryptology was still developing), so people might have not thought in a “numbers now represents syllables” way just yet. A reason for the people's unfamiliarity would be that since the Great Cipher was made by two people (the Rossignols) who already knew how to crack extremely hard ciphers, their knowledge of the weakness of strong ciphers bolstered their knowledge to build something knew that didn’t fall into the traps of the simple mono alphabetic substitution cipher. As such, because they thought five steps ahead of everyone else. In addition to their death, the Great Cipher remained unsolved for 200 years because the only people smart enough to crack hard ciphers and used the weakness of those to create a new super hard to crack cipher had died. In short, their knowledge of the Great Cipher died along with them until it was unearthed 200 years later.