I may be wrong but I would assume the problem is that people are sitting on a boat for hours going from zone to zone macroing allowing them to fish in multiple zones catching a variety of fish without having to worry about fishing becoming trivial in a particular zone and not having to be there to do it.
Would it be possible to change the way you can fish on a boat. Maybe make it so that each time you zone it does something that would disrupt your ability to fish. This small thing should be quick to fix but would disrupt somebody who had just had fishing macroed and wasn't at their computer. For example maybe have it that you can only fish from a certain part of the boat and each time the boat zone it would move you to the another part. For someone there it will take a sec. to run back there, but I couldn't think of a way a person with a macro could have it automatically set to do that. Or maybe have it that you have to get the ok to fish from a NPC on the boat in order to fish and have to rehail him every time you zone. Or maybe have it that when you zone into a zone you are set to automatically be sitting (since I'm under the impression you can no longer fish sitting).
Not sure if any of these options would be viable but it just would suck to lose fishing on the boats since the the trips can be pretty boring without anything else to do all because of a few lazy a-holes messing it up for us all :sadf: .
Honestly, the only thing I can think of is to make it impossible to skillup while fishing on a boat. We can discuss ways to implement boat fishing in the future, but it needs to go away for now.