A statistical analysis of the unsolved Zodiak killer cipher shows that it is like fake ciphers and unlike true ones, such as the Zodiak's other, cracked ciphertext. In the chart above, created by Tom S Juzek, the red dot is the unsolved cipher, the purple dot the solved one, the other squares known-true ciphers and the diamonds known-fake ciphers. [via r/codes]
In my view, the most likely explanation is that the cipher is a ruse. Serial killers tend to be subject to hubris, as Douglas points out in his excellent book on the subject [html link]. It must have been a shock to the Zodiac Killer when he learnt that his z408 cipher had been deciphered so quick, by two hobby cryptographers. To prove intellectual superiority, he needed another cipher, one so strong that couldn't be deciphered, certainly not as easily as z408. I think the Zodiac Killer was unable to produce such a cipher, which is why he chose to take another route: He decided to cheat. The Zodiac Killer created a fake cipher that no-one could ever decrypt.
If you're wondering why the cracked Zodiak cipher is way past the rest of the "true" ones, it's because they all involved more randomness than his--never roll your own crypto. Be sure to read Juzek's post as it's staggeringly thorough, yet interesting to someone like me who knows nothing of mathematics.
Compare to Craig Bauer's solution, which Juzek describes as "far fetched."
Here's the original, if you'd like to take another futile stab at it: