First I think it is important to distinguish between the sort of rote post-communist TCM that is taught in schools and Chinese Medicine which is the lifeblood for all of the systems. Japanese acupuncture, for example, is the growth of Chinese Medicine as it was offered to them in the early 1000 ad's and then brought up through their own culture with their special skills and talents and further honed by multicultural exchanges with professionals around the world. The same with French, Korean, various microsystems, even our own Tam Healing System.
While we call what we do "TCM" out of convention, we use nearly all palpatory diagnosis (abdomen, points, areas, etc.) and rarely use the tongue, pulse, etc. And from my sense of it, this is still Chinese Medicine.
With regards to treating the root first, etc. - I believe that this is part of all systems it's just better articulated and preserved in Japanese systems - particularly at the level everything is taught in schools. That said proper "TCM" is pattern oriented not symptom oriented which depending on how deep you look for the patterns it should be the same as treating the root. Don't forget that Japanese systems also have local, "i.e. symptomatic" treatments as well which are generally performed after the root deficiency treatment. In TCM you are often mixing root and local "ashi" points at the same time - one of many reasons for more needles. It is important to note, however, that many "TCM" practitioners use very limited numbers of needles - so that's not a fixed difference between the two systems.
All that said, I agree with you that there is an incredible amount of finesse and beauty in the Japanese system. And learning from all of these systems and using techniques from each is a good goal. In the beginning, however, it is often best to simply stick to an entire system so you can learn it deeply before you start pulling in techniques from anywhere.
With regards to needling, as evidenced by other posts I've made, I'm a huge fan of simple, painless needling. While I was trained extensively in Japanese acupuncture, I now use the Tam Healing System in nearly every case. From the Japanese system I brought the skills it offered in palpatory diagnosis and light needling technique primarily. I do use 36 gauge Chinese needles for the most part but with Japanese insertion techniques, depth, and palpatory feedback.