Aha ! My specialist subject..... Retargetting can be done in realtime but its difficult and expensive as involves a lot more than just rotating stuff. Basically you need ik and you need target positions for any node that's important eg. feet. its not too bad if skeletons share the same hierarchy but is a minefield if…
could you re-target animations to a different sized rig with an identical structure? XSI has this capability, not sure about other packages since i'm by no stretch an animator ;-( fx.: http://www.kxcad.net/softimage_xsi/Softimage_XSI_Documentation/mocap_RetargetingAnimationfromRigtoRig.htm