Combining the transfer functions in any way is likely not a valid approach. (You have not posted your code, so I do not know how you are estimating your transfer functions.)
The tfest (link) function (in R2012a and later) allows you to specify the number of poles and zeros. I would specify the same number of each for every experiment, being sure that they are specified so that the transfer functions are always proper.
Those transfer functions will each have the same number of poles and zeros, so you can then look at the poles and zeros directly (in z-space on the unit circle or in s-space in the complex plane). If the poles and zeros appear to ‘cluster’, the best approach might then be to take the complex mean of each cluster, and use that to define a common transfer function. (You could use the kmeans function to define the clusters, if you convert the imaginary components to real values first. The coordinates of the centroid values kmeans returns may be all you need to define your poles and zeros.)
NOTE — This is entirely conjecture on my part, since I have never done anything like what you want to do. I cannot claim that there is any mathematical justification for it. I invite you to experiment to determine if it would appear to be a valid approach with your data.
