You'll probably need to be more specific. Traceroute generally has 3 probes per hopcount. How do you want to show the differences? Between the smallest of one set to the largest of the other?

And what if the route flaps in the middle (where you get a new host on a given line)? How do you want to see that?

And what if the route is different from one view to the next? The hop-by-hop counts will be relatively unrelated after the first branch point.

So, if you can explain (as in provide a specification) what you mean by "count the route differences", you might get a more concrete answer rather than all the handwaving responses so far.