There are lots of fish that are still unstackable - Gugru Tuna and Grimmonites come to mind immediately, but there are many others. Even some tiny fish like Elshimo newts are unstackable for some reason.

I think that these stackable fish should still only stack to 12, however, and not 99.

I understand that these are ranked fish with size data embedded in the item, which makes this tricky. Perhaps there could be an NPC in the Fishing Guild who can measure a single stackable fish to convert it into the unstackable variety, with size data, for fish ranking.

Choosing to be able to sell a stack of 12 or a stack of 99 on the auction house would be nice. However, I suspect this mechanism is fairly deeply embedded.