I came across this article about the future of Yellowstone's trout. After taking comments from the public, it looks like the Park Service has a come up with a draft plan for future trout management. Seems pretty reasonable to me (haven't waded through the details though).
Lake trout have become a huge problem in the park and hopefully these recommendations will help reduce their numbers, allowing the native cutthroat trout population to rebound. Also, reintroducing native cutthroat and grayling to historical waters makes sense, although it's interesting that the Madison, lower Firehole and Gibbon rivers wouldn't be included. Historically, these waters contained native cutthroat trout and grayling, while no fish resided in the upper Firehole (above the falls). I imagine that people wouldn't want to see such a world class brown and rainbow fishery destroyed (Selfishly, I don't know that I would). Plus, I don't even know if it would be possible, for the brown and rainbows have been residing in those waters for close to 100 years now, making them full fledged Yellowstone residents.
If you're interested in Yellowstone and its fishing history, Yellowstone Fishes- Ecology, History and Angling in the Park by John D. Varley and Paul Schullery, is a great book to read.