Walli's answer is accurate. It really depends what purpose you need the hierarchy. If you are doing a commercial film that needs a tree growing from scratch, then you would study the growth animation shown in the tutorials section and use that as a basis to build your own . The existing libraries that are pretty much all 3.5, are best edited in 3.5, e.g. that would mean to change branching, gravitropism, trunk lengths, etc, to create more variations. If you just need wind effects, we see users applying dynamics to hierarchy models all the time now. It really is a question of what you want to do with the hierarchy, what needs that you have, decide what software to use. It is also possible to open a model in 3.5, study it, pull it apart, and then rebuild side-by-side in xfrog for maya or xfrog for cinema4D- normally i would say import hierarchy and tweak, but its also possible to study the hierarchy in detail in 3.5, then reproduce it in maya or c4d - but again, depends what you are really needing to do with the hierarchy. in any case i hope you have seen Walli's new video, Building and Animating a Rose using Xfrog Cinema4D.
http://vimeo.com/39361651