Before starting giving you tips to do it, I wouldn't recommend you animate bones because it's not convenient at all, specially if those joints already have animation.
Anyway, animation layer could do the job, but keep in mind a joint chain is fully FK so if you rotate a bones it WILL influence his children.
Another idea is Constraint (Parent, Position, rotation) but it will override the animation. What you can do instead is creating a controller( Nurbs curve or whatever) for each joint, copy the animation of the joint into the controler and then parenting the bones to the controller. This is basically trying to rig the bones structure again, not super practically either but is better than animating bones directly.
Hope it gives you some ideas to do it, in any case I wouldn't like to control baked joints but here is some thing you could do.
Zablorg, there is a discussion posted a while ago that someone was trying to find out how to simulate for games, since it's so memory consuming. There's been said that you could parent the joints to the geo, simulate the geo, bake the sim to the joints and then un-sim and unparent the joints, so, after all the simulation would have turned into an animation saving lots of memory.
My rigging is all max based but I did this many times by driving another rig off the simulated joints and using weighted blending on controllers to edit the result - you could do the same with animation layers if maya doesn't support controller blending.
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Anyway, animation layer could do the job, but keep in mind a joint chain is fully FK so if you rotate a bones it WILL influence his children.
Another idea is Constraint (Parent, Position, rotation) but it will override the animation. What you can do instead is creating a controller( Nurbs curve or whatever) for each joint, copy the animation of the joint into the controler and then parenting the bones to the controller. This is basically trying to rig the bones structure again, not super practically either but is better than animating bones directly.
Hope it gives you some ideas to do it, in any case I wouldn't like to control baked joints but here is some thing you could do.
Cheers