I've only played Japan so far, regarding the sphere issue; Spain, the USA, Russia and France did influence me slightly, however it was half-assed.
Looking at the bigger picture;
All GP's fight over Egypt and Columbia because of the Canal decisions.
France and Britain battle over Belgium.
Russia and the Ottomans battle over Persia(between forging CB's on each other)
Prussia and Austria battle with each other, as well as France, over the German minors.
The USA likes to focus on Haiti/UPCA/Mexico/Hawaii- the nations on its continent.
Seems logical to me that Japan would be a low priority until -
Belgium GP's so France and Britain focus elsewhere.
Germany forms
The Ottomans drop into secondary power status leaving Russia free to sphere Serbia and the Romanian principalities.
The USA takes it's cores, annexes Hawaii, spheres North America.
That said, during vanilla Vicky, I rarely got Sphered as Japan until Russia claimed Sakhalin and had a border with me. SO hardly seems a new issue to me personally.
tl;dr - Japan despite being arguably the "best" unciv, isn't worth the GP's attention until they've consolidated elsewhere. Far more profitable for them to sphere the nations they do as opposed to the Island Unciv with the cool flag and history.