The proposed changes have come about. Admittedly it only effects a small number of rivers and small sections at that, but the changes are significant. The latest Fish and Game Newsletter had a snippet:

A heap of Designated Waters Licences have also been sold.
The Designated Waters system has replaced the Backcountry system and is designed to see Kiwi anglers get a fairer share on some of the waterways that Fish & Game’s research has shown are subject to too much pressure – around two per cent of the country’s rivers.
The new licence category will help us manage angling pressure by spreading angling effort around so that it isn’t concentrated in certain areas, which detracts from the angling experience and also has the potential to negatively impact the fisheries.
Over the past ten years, Fish & Game has received increasing complaints from resident and non-resident anglers regarding overcrowding in a small number of fisheries that will now be managed through the Designated Waters Licence.
Our research and monitoring show that a small percentage of non-resident anglers will intensely fish in a local area, putting pressure on the fishery and displacing other anglers. We’ve implemented this new fisheries management tool to help address that imbalance.
In some fisheries, angler use has gone from a roughly 50:50 resident-to-non-resident split (in the early 2000s) to an 80:20 split favouring non-resident anglers. In most cases, pressure-sensitive fisheries, now managed through the Designated Waters Licence, share common features. The rivers have very clear water, offer excellent sight fishing, hold large average-size trout, have high scenic value, and are often located in a wilderness or backcountry setting.

These Designated Water Licences are only available for those with a Season Licence. I’ve not been able to see the authoritative cost/conditions but this article by South FlyFisher may be correct.

For those who frequent Southland the only Designated Water is the Upper Oreti. More information here.