wow, what a long post...
anyways...
after u create an animation clip, like a walk,
when playing back the animation, u can still set keys on the legs.
for example, like u said, a footbal player running and dodging, u can simply create a run cycle, and make him run, and when he needs to be animated dodging other player you can simply set keys on what ever leg attribute you want, the run cycle will remain intact. because the trax editors clips are independent from the key you set in maya (keys that are key framed normally)
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very simple and effective. just becareful on how you set up and approach some things.