Unfortunately subcharacter sets can cause problems of their own. I distinctly remember having problems like subcharacter keys not showing up in the timeline (or maybe it was the graph editor or dopesheet). In any case I remember trying exactly what you propose (subcharacters for arm, leg, etc) and not being happy with it.
For now, I generally use only 2 subcharacters; face (blendshapes) and pose.
I usually animate in the pose set, with autokey enabled. That gives me two fairly intuitive ways to set keys; I can set efficient keys just by moving the model, and use the keyframe button to set poses. If I really want to mess with the timing of one particular item or group of items, I toggle in and out of the character set as necessary.
So I guess that's my take on it. Character sets are not the 'best' way to set keys and probably aren't intended to be (keep in mind that they are ultimately a rigging device); from an animation perspective they are one tool among many, and in that context they work fine.
Of course, I'm just a student, so what do I know =)
On a side note, character sets can really screw up items with quaternion rotation interpolation. It always bugs me that two of my favorite features don't work together.