Threre are a variety of ways to deal with your issue. To discuss what you're after, sure, it's not that hard. You have "skeleton A", that has mocap. You can dupe that skeleton, get Skel B. Put the various kinds of rigs controllers on Skel B that you'd like. Then, parent those rig controllers to Skel A. You have Skel A "puppetering" Skel B, but you can still animate Skel B's animation controllers providing an additive offset.
I use that method to "tweak" mocap. But the next step I use is a script that physically retargets the mocap onto yet another rig, the "animation rig" our animators use. The script takes the rig, and per frame, matches it back to "Skel B", "transfering" the animation across. The cool thing is, it can transfer the mocap on to any animation solution on the rig. As an example, we have FK arms, IK local space arms, IK global space arms, etc. During the transfer, you can put the mocap onto any of the different solutions, depending on what you're after. As well, this retargeting solution allows for the mocap to get dumped onto any of our characters.
I hear trax is improved in 6, but it still leaves a bad taste in my mouth. I still avoid it.... always seems to cause more problems than solutions.
I've played with M6's animation transfer ability. It's well thought out, but not quite what I was looking for.