While I do reference the class A list, I generally don't use it as my "core" list. Many of my favorites are NOT class A. Especially when talking smallish, freestone brookie streams.
A couple of reasons:
1. These populations swing wildly, and they aren't sampled by the PFBC all that often. So a snapshot of what it was like in 1980 or something is hardly a good predictor of what it's like today.
2. When they are sampled, the whole thing may not be sampled. If they shocked the area down by the road, that's fine, but I'm probably fishing a mile in or so and it's less likely to have been sampled.
3. How it rates in a "class" can be inversely proportional to the agressiveness of the fish. Class A streams tend to be more fertile, and the fish pickier. With the standard tactics for brookie streams, you're relying on aggressiveness, so more fish to catch doesn't equate with more fish caught.
4. How it rates in "class" can have more to do with the structure than the number of fish seeing your fly. You don't fish the unproductive looking water anyway. They rate it by biomass per surface area, not biomass per volume of flow. Narrow, deep streams have an advantage, and will be rated higher than a stream carrying the same amount of water, with the same amount of fish, that's a little wider and shallower. Also, some streams have ok holes every few feet, and others have good holes every 200 feet. But having more "walk past" water doesn't lower your total much, streams with more fish per "pool" fish better, even if pools are farther apart. The goal is number of fish seeing your fly per cast.
Anything on the wilderness list is generally pretty good, even if it's class B or C. There's lots of other good ones though. The streams with natural reproduction list is my "base" list. Then narrow down the best you can with other factors. Higher gradient is generally better. Farther from roads is generally better. Sometimes you hit on a little geology, i.e. the streams in a drainage originating from the south may be worse or better than those originating from the north. Then you look up geologic maps and determine what rock formations may cause this effect, and extrapolate.