There is a solution to this problem in: "Comparing and combining time series trajectories using Dynamic Time Warping" from Neil Vaughan & Bogdan Gabrys.
It uses a Dynamic Time Warping (DTW) algorithm which tells how the points on trajectory A can be mapped to the points on trajectory B with the least "warping". You then compute an average of trajectory A+B by averaging the points in A and B that DTW has "paired". If you have more than two trajectories, proceed iteratively: first, merge A with B, then merge C with the result, and so on.
There's a good implementation of DTW in R (library dtw
)