I think a couple more words for new animators might be helpful.
Retargeting is just the process of “copying” the animation from one skeleton to the other. As you probably know, the simple cut and paste of keyframes between characters do not work. The joints might have different names, might have different rotations, different zeroed rotations, positions, etc etc. Some real time engines are able to do this with very strict rules of how the skeletons must be made, most of the time the difference are just and only the proportions, where just the rotation of the joints (except the root node) are used between skeletons that are mostly equal.
When characters have different skeletons, even with different hierarchies, you have to use some sort of tool, like Motionbuidler. The way it does is to have two characters in the scene, and copy it from “one control rig to the other”. If you haven’t, you should familiarize yourself completely with Motionbuilder’s characterize tools, since they are essential to fully use the software. Characters in Motionbuilder can have many inputs, like an Actor from mocap software, the control rig, which is used to animate or edit the animation of a skeleton, or another character, to “retarget” the animation from this character to the current one.
Getting into more detail, to do this, you import or merge both skeleton hierarchies into one scene. You characterize each one of them, correctly. They need both to be on tpose, and ideally should have all their bones above ground (above 0 y). Refer to Motionbuilder help for this, it’s thoroughly explained there. And this is one of the tricky parts, to use the retargeter script, each animation to be imported must be on tpose on frame 0. You don’t actually need to create a control rig for each one of them, after both are characterized, you just need to select the input type of the new character to the old character, and activate it. Animation on both characters should then be synched, regardless of differences in hierarchies or proportions.
The retargeter script just automates this process, loading a folder containing .fbx or .bvh animations over the new character. It does characterize the animations if needed, but they need to follow either Motionbuilder nomenclature or 3dsMax Biped to be correctly characterized. If they are not, you can just edit the Motionbuilder one inside the script, changing the right column to match the names on your skeleton. You don’t need to change all of them, just the ones present on your skeleton (if you don’t have finger animations don’t bother, for example).
You can, for example, get all or some of the 2600+ mocap files from Carnegie Mellon University Motion Capture Database at cgspeed.com, which has .bvh’s and .fbx’s with a tpose on frame 0, and with the retargeter script quickly retarget them over your character.