Both of these disputes (and a few others) are about possession of the oil and gas resources under the South China Sea.
If the world is to avoid warming beyond 2C, all of the oil and gas under the South China Sea needs to stay buried there forever. If China and Japan resolve their disputes in any way that grants either side actual exploitation rights, the world will take one more small step towards being fucked. Some scientists are now arguing that even 2C is going to cause catastrophe; we need to get even tougher. This means that the best thing for the world is for China and its allies to continue locking horns over these islands for … about 1000 more years.
The best thing China, Japan and the Philippines can agree on is that exploiting these islands is against everyone’s interest. The whole region should be set aside as a marine park, and the military forces of every side of the dispute put to the task of sinking any oil research vessel, fishing boat or seismic survey ship that comes within a sniff of the place.
But that’s not going to happen, is it?