Acid rain is already waning. At first it was due to better scrubbers on coal power plants, and I'd expect the trend will accelerate now that we're totally shutting down a fair % of the coal plants. I recognize much damage is ir-reparable, as it's loss of buffering capacity. In that way the effects of acid rain are somewhat cumulative, rather than dependent on current rain. i.e. improvement means you've slowed down, not stopped the damage, nor reversed prior damage. So there's more to do but it gets harder from here.
I don't think we're really near the case where you can get the big streams back. I do think that's possible to see some improvement in the still forested watersheds, but it just takes time. A lot of it. Waiting for the forest to fully mature and the soil to build back up. So, like, centuries, with little that can pro-actively be done.
You can adopt smarter management practices. Such as identifying those streams which can have stronger wild populations, and changing management to maximize it. This is in the realm of whether or not you stock it, creel limits, seasons, etc. I think of good management as mostly short term, though. I mean, yes, it affects how good the stream is. But I have doubts on whether good management actually seeds new populations, merely strengthen current ones. And I have doubts on whether bad policies will eradicate any current populations, merely weaken them. Stop fishing altogether and the streams revert to whatever they're capable of within a mere few years. i.e. in the long term, big picture, you're not really gaining anything here.
There's work to be done regarding farming practices. Fertilizers, insecticides, etc. I think there's a few streams we could probably gain back or improve this way. But, to be fair, MOST of the current brookie streams don't have much in the way of farmland. This is an important topic but the greatest gains will be on larger waters, which, due to brown trout and forest/water temp, are still likely not to be brookie water.
AMD remediation, of course. Doesn't affect non AMD areas, but still, there's a pretty high number of streams we could gain back this way.
You could get aggressive and pro-actively attempt to remove brown trout populations and seed brookie populations in their place. I don't know how successful this would be, and my gut says it might work short term but it'd take "repeated" application to keep it that way.
Long term, the biggest danger is clearly simply development stemming from population growth and sprawl. Replacing forests with farmland, housing developments, commercial areas, new roads, etc. Many of the impacts of gas drilling fall in this category, as jobs in rural areas = growth in rural areas, plus pads and access roads are a form of development centered on the areas we care most about. I don't pretend that you can totally stop development, nor that you should (people are more important than fish to me). But you can strive to minimize the impact, and be smart about how you do it. Protect the most important lands. Riparian buffers. Sewage facilities. Building practices and drainage controls. Stuff like this can severely slow the inevitable damage. And there are plenty of examples of brookie streams in relatively populated areas that prove they can coexist with us, maybe not in a fully healthy situation, but a sustainable one.