Because Japan has realized that it can't hold Chinese coast-guard boats at bay any longer, and now Chinese boats can cruise around Diaoyutai any time she wants to, almost without let or hindrance.  So if Jap keeps on dispersing the fishing boats of Taiwan as it used to, how should it tackle with the situation when Chinese boats are trying to protect her little brother?  When that happens, Japan, as well as its master the U.S., dare not to confront the challenge from China, and may thus tilt the balance in favor of Taiwan/Mainland cooperation.  That's why Japan reluctantly let the protracted "Japan-Taiwan fishing talk" have a "breakthrough" and sign the agreement.  (A Taiwan official shamelessly declares that from now on Taiwan's coast-guard has the right to "disperse" Chinese fishing boats around Diaoyutai when necessary. It sucks!)

Some critics said that the Republic of China acquired the fishing right at the expense of sacrificing our sovereignty over Diaoyutai.  Don't worry.  The sovereignty of those islets belongs to China, China on both side of the strait.  Therefore, the issue is still at large.  Let's wait and see who has the last laugh.