Hah, thats funny, because most of the work I do with motionbuilder, I WANT to stomp on the data. However, I work in video games, and we need to make the motion NOT look like mocap if you get what I mean. I use it mainly for Layering motion. Which maya cannot do very easily.
It’s been a while since I worked in games… but I don’t really know why you would want to stomp on the data and have it “not look like mocap”. Why are you using mocap if you don’t want it to look like mocap - why not keyframe or roto animate to the mocap?
From my [little] experience in the games industry, the worst stomp on the data comes from curve fitting compression on euler f-curves, which is just wrong for so many reasons. In that case then yeah, you’ll need to stomp all over the data to avoid parkinsons or other artifacts.
Yup, layering can’t be done very easily, but there are ways to do it (without using the trax editor).
When I need to get straight data from a capture that needs minimal editing where we’re not destroying stuff, we Process it with IQ then send it straight to maya and put it all on a rig.
Do you export the skeleton data as a V-file and apply to the rig? If so how did you get around the z-up problems and rotation order? Or if you export at trajectory data, how do you get it on the rig?
We’ve actually recently tried your Peel software to compare it to what we’ve made. Looks promising. Good luck with it.
Thanks… let me know if there is anything I can do to help. Wanna buy a copy? 
P.S. we’re hiring mocap specialists ( Leads, Shooters, Trackers/Solvers etc ) Brand new Vicon system in house. Message me if you fit this position.
I used to live up the road from you… I was living in Laguna Beach and working in San Clemente on barnyard. I’m working at the Film School in Vancouver now taking a break from production. I’ll drop you a message if things change and I get the production itch calling me.