Jeff Murray likes this time of the year because the large trout feed well. Just remember the Brook Trout are well underway with their spawning by mid-October here in the mid-Atlantic area. Please refrain from fishing the native Brook Trout streams until late February (the eggs have hatched by then).
As the trout streams start getting colder an easy way to stay warm and comfortable is to wear a 200 weight pair of polartec pants under your waders.
When the leaves fall heavily on our smallmouth rivers in the fall they often become so thick on the surface of the stream that fly fishing can be difficult. However, I often whip this problem by fishing spots where natural stream features block the flow of leaves from the surface just downstream of them. Three of these areas are river-crossing ledges that extend above the surface of the water, back eddies and log jams. I simply wade in below these areas and get excellent fishing.