Should be resolved soon. A bit less incompetence and ass-covering from the Philippines and a bit less grandstanding from Ma and the whole affair could have been resolved with a lot less unpleasantness. Better late than never I suppose.
That's too optimistic, in my opinion. We are seeing signs of Philippine trying to back down now, but there is utter lack of trust from Taiwan. There is suppose to be parallel investigations by both side now, Taiwan now insists on everything being agreed to in writing before allowing the investigation to proceed, based on Philippine's prior snub and reciprocity. According to Taiwanese, there are 11 issues submitted from each side. Taiwan agreed to 9 and rejected 2 -- and one of that (interviewing the crew) was rejected because Philippine would not allow their crew to be interviewed. The other issue is new autopsy, with Taiwan rejected on the ground of decency and family opposition, but Taiwan will release the autopsy video to Philippine investigators. Philippine, however, rejected 9 out of 11. Hence Taiwan put a hold on the permission on account of reciprocity.
When the investigation complete and the Filipino crew formally charged, I expect Taiwan to demand extradition, and Philippine is expected to refuse. Why? Because in 2006, after another Taiwanese was killed by Filipino coast guard, the persons charges disappeared in the middle of their trial. And there are other potential traps -- judge rule in favor of the Filipino, Presidential pardon and/or quiet release- after the current crisis is over. Given the climate of distrust, I don't expect Taiwan to give in easily.
I don't really know what the 'swaggering, overbearing, tin-plated, demagogue with delusion of godhood' (Noynoy Aquino) is thinking. But I don't see how he will come out of this with his popularity intact. But he knows Filipinos better then we outsiders possibly can. [That, by the way, is a paraphrase from Star Trek, the original series. Bad taste, to be sure, but just couldn't resist.]