Interesting, which packages did you try running it on for which it took too much execution time? Where was most of the time spent?
Now that I think about it, it's quite possible that the process was apparently hanging on the same issue I describe in my article, where babel-core depends and babel-cli and vice versa. Maybe it would work better if I were to run the process a first time with a simple algorithm like the one exposed in the article, that would clear up any dependency loop, then a second more complex pass that wouldn't have to deal with this.