Several solutions have been discovered towards this "in-betweening" effort including but not limited to key framing, linear interpolation, motion re-targeting, and even manually animating every frame. However, each of these solutions are costly and time consuming. Using quaternions and a form of linear interpolation, a mathematical approach was used to “blend” two independent animated sequences and aid in streamlining this process.
Using the basic guy rig found at The 11 Second Club, I was able to test my algorithm and verify it's success. Following you'll see the videos demonstrating the "in-betweening". The first video uses the basic guy rig where I 'motion merge' the basic guy from a standing position to a sitting position. The second video uses two completely different objects (a cone and a cylinder) where the first object is animated to merge in to the second object's position.
Basic Guy
Cone-to-Cylinder
There you have it! Motion merging was a really fun topic to work on. I'll try and post more details on how the algorithm works at a later date.