Im confused with what your using motion builder for, actually cleaning the mo cap data or animating with it?

If your cleaning up raw data then motion builder makes it so much easier as you can set up rigid bodies to help out you out with occlusions, theres also the swapping that motion builder does for when your markers might get swapped, I cant even think how you would go about this with maya.

It took me a while to get used to motion builder, its a shame as 3d buzz had some great tutorials on the that were free, but they've gone offline, but I really like it, I pretty much wouldent animate in maya after using it, (I do a lot of motion capture onto characters)