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Let's say you want to interpolate the movement of empties between frame 0 and 50

1. create one empty for each tracking point of set A.
2. add a constraint to the empty associating with tracking point 1 of set A
3. add a constraint to the empty associating with tracking point 1 of set B
4. set the influence of the first constraint to 1 and add a keyframe
5. go to frame 50, set the influence to 0 and add a keyframe
6. do the inverse of steps 4 & 5 for the second constraint (0 --> 1)
7. Repeat steps 2-6 for the other tracking points

This strictly answers your questions of how to interpolate between tracking points (you might need to adjust the curves to be linear).

However since you need to morph the next logical step was to use the empties as hooks to deform a mesh. However the hooks need to modify the position of the vertices directly and not relatively as they do (see this queston ). Still, the half-solution here is worth sharing.