I have 2 almost identical skeletons with an incredible number of bones (for facial animation). One of the skeletons has a few more bones than the other for body animations. I want to use IK rigs to retarget the animations. However this would require me to create a new retarget chain for each bone on both meshes. There are a whole lot of bones so I was wondering if there was an easier way to do this (they have the same names).
Hello take a look in learning, you’ll see in fact is not so complicated 
If skeletons are similar you can try right click and retarget, but i always recommend to do it by hand, the reason is the results are better
In here at the bottom of the page you can see it
I just got done doing something very similar. Here’s what I did:
I created a single IK Rig for my main skeleton. I then opened up this skeleton and went to Window->Asset Details and added the other skeleton as a ‘Compatible Skeleton’. If you do this for all the skeletons you want to retarget to/from, you only have to create the IK Rig once and you can copy it for any other skeleton (that is compatible) - just switch the preview mesh for each copy.
Also, I’m no expert, but I’ve had great results with just creating the most obvious chains and leaving the rest alone. Arms, legs, spine, etc. you need, but sometimes twist bones, IK Goals, etc. are overkill.
Hope this helps.
The problem is when you need to adjust something like the fingers
Then you have 20 animations to fix instead to do it in 5 min
And that kind of little details appear when you almost finished 
interesting. this is for facial animation however so i will need to include all of the bones.
hmm. im not sure what ur refering too. maybe I missed it.
