Great topic. I fish some of the more popular streams and rivers, popular by means of floaters. Most of the water that I prefer to fish is your basic rock with current on one side with some depth and mud/sand with some brush on the other side.
I catch more numbers from the current/rock side but most of my bigger fish ( I consider anything 15" and over my bigger fish ) come from the shallow muddy side. Most of the time the fish are loners and are holding on a isolated piece of cover. 9 times out of 10 they will be sitting right in the shade.
So to answer your question I guess it depends on the time of day. Mornings/overcast I prefer to fish the tail end of runs with rocks. Midday/evenings shallow wood/grass.