After browsing through the WAP, which is not the easiest reading, this is what I have gotten from it.
NJ has identified of course the threatened and endangered species which are already protected. It has also identified species of animals, birds, plants, fish, etc...that they feel are threatened or on their way to becoming threatened! This includes a handful of freshwater and saltwater fish. They have broken this WAP down into regions. Some species are region specific and not statewide. The State has not come up with a set plan, nor have they noted any regulations on these species yet(except threatened/endangered species and the sunfish regulations for 2008).
At this time, I don't see anything that is going to affect saltwater sportfishing, but there are some baitfish on the list. There are some other species on the list that may also affect fishing indirectly, but right now there are not any pans in action, just identification. The list of fish species are: Hickory Shad, any anadromous fish, Marginated Madtom, American Brook Lamprey, Bridle Shiner, Brook Trout, Brown Trout, Comely Shiner, Cutlip Minnows, Ironcolor Shiner, Rainbow Smelt, Shield Darter, Slimy Sculpin, Banded Sunfish, Blackbanded Sunfish, Mud Sunfish, Pirate Perch.