The disease at the hatchery this year was a setback for NJ F&W, but there are still plenty of opportunities to catch both wild and stocked trout in NJ. F&W has taken some reasonable steps to mitigate the stocking situation, and there will still be a stocking of 500k+ trout. More trout have been stocked in water that is strictly put and take and closer to populated areas, which in itself may be a reasonable long term pattern. And the idea of the upper SBR down to Long Valley as a WTS as mentioned by Rusty is a great idea - perhaps a year or two of no stocking may help this happen. And the new C&R on the Flatbrook, which has some wild brookies and browns, will only see rainbows for a while which have never been known to reproduce on the Flatbrook. Coupled with the no-kill regulations, the wild trout will not have stocked trout around to interbreed with which can hurt the wild strains. It will take at least several years, but we should see more and larger wild brookies and browns on that 4 mile stretch - I say stock rainbows only on the Flatbrook C&R as we monitor the progress of the wild trout over the next decade.
So this is not Armageddon, but a forced change in tactics by F&W from which we may learn some new ways to better the trout fishing. The staff at NJF&W is doing the best they can, and are dedicated professionals working to protect our wild trout fishery and also satisfy the anglers that want put and take fishing. If the design of the open runways allowed the infection of the trout of disease from bird droppings, I am confident that it will be mitigated and that more disease resistant trout will be sought to replace the current cultured browns and brook trout at Pequest.
Speaking as a NJ resident, the cost of the fishing license and trout stamp is still a bargain, providing plenty of wild trout opportunities (if you take the time to look), plenty of stocked and hold over trout on some waters with great hatches, and more than enough stocked trout on marginal waters to satiate the meat anglers. We have lost some waters in NJ due to development, but quality trout fishing opportunities in NJ are better than 50 years ago, and for those of us in North Jersey, less than a hour away.
One last comment, those of us who do the majority of our trout fishing on small - mid sized trout streams for wild fish know that you have to add stealth to your fishing arsenal. As wild trout populations in waters like the SBR, Flatbrook, Pequonnack, and Wanaque hopefully rebound, expect a different challenge.