It had the downside of requiring precise timing. This is an issue if you wanted a faster (or even a slightly improved) 6502 in the machine.
Oh well...
No, the Disk II was absolutely a masterpiece. Go back to the linked article, think about everything this very complicated chip did, and recognize that Woz made a card that did exactly the same thing out of 6 chips you could buy at Radio Shack and two tiny ROMs.
I don't consider it a mistake - nobody at the time was realizing that we all would, eventually, move our software to faster computers every couple years. Woz is brilliant, but he couldn't have foreseen it and, as you point out, almost nobody did.
https://en.wikipedia.org/wiki/Apple_II_accelerators#Zip_Chip...
With current tech it should be trivial to keep all of the RAM in the module and just asynchronously push some writes out (video and IO) at Apple II speeds.
Seems like if you're going to reverse an obscure chip, something with a more exotic application would have been more fun?