If I were head of the Japanese federation, here's what I think I would try:
It would not be impossible for the Shibutanis to skate for Japan and start a Japanese dance tradition. Because Japan is so strong in both men and ladies, there are plenty of great skaters that could take up dance-what's missing is the infrastructure of great dance coaching for intermediate & senior levels in Japan. And all that takes is for one or two great coaches from somewhere else to immigrate to Japan. The Japanese federation is reported to be doing well. They could actually pay to set up dance coach/coaches in Japan.
Look at the US, and look at how Shpilband & Zoueva (AFAIK, without any US Federation help) have built a world class dance program in a country that was mired in the 7th to 10th place at Worlds at best. Yes, it can take a decade (if they make an effort, it should take no more than that). But if the Japanese recruited the Shibutanis (even if they wait until after the Shibutanis become senior-eligible), they'd have another leg up.
In pairs, the Japanese junior pair did make the JGPF this year. Given that 5 of the 8 teams were from Russia (and therefore only 3 of them can make it to Jr Worlds), the Japanese could place in the top 6 to 10 at Jr Worlds, so Japan already has the beginning of a pairs program.
Again, they need a top pairs coach.