Personally, I think the acid rain has had an negative effect on fertility of the Smokies streams and therefore the size of the trout. Warmer stream temperatures has also had a negative effect in my opinion.
Last year I read a report of the Kg/Ha per certain Park streams and was a bit surprised at the numbers. I believe Deep Creek only averaged 25 or so and that is very ordinary and average in the Southeast. It is nothing like the "gem" status it used to acclaim in the 1980s and prior.