Well the capture and public display of Allen Pope did wonders at the time... that and the fact that the TNI of the time is also a somewhat capable and reliable power (at least compared to the rebels or communists)... But still, in the end the US got what it wanted, the removal of Soekarno, the rise of Soeharto and the change of our political orientation after the G30S movement, and as a bonus the destruction of the 3rd largest communist party in the world + destruction of TL as a potential communist base in SEA... and with minimal cost too.. Of course after Suharto is no longer useful he'll have to go too...
PRC aggressiveness in SCS is a matter of concern of course, but so far is mostly a matter of border friction and overlapping fishing claims rather than any full blown invasion threat... We can continue countering it with what we are already currently doing, but perhaps with more haste... Continue the build up of the Natuna base with better equipment and alutsista.. Increase regular patrols in the North Natuna Sea (both by Navy and Coast Guard), increase surveillance of the area through air patrols, drones, and satellites even, increase military trainings in the area (preferably with other ASEAN countries as well from time to time)... increase the number of our fisherman fleet in the area + educate and provide them with comm gear to act as another layer of surveillance... increase the civilian maritime infrastructure in the Natuna islands (Ports, Fish processing, Ship repair, Storage, Fuel depot, Electricity, Telecom, etc)... Increase gas / oil exploration and extraction activities in the area...
Diplomatically PRC is already isolated in the SCS issue (no other country is supporting their claim) so getting any diplomatic support should not be an issue, but we need to work better with other ASEAN members (at least with those having the same issues) so that we can speak in one voice against these PRC incursions... Publicly protest every known incursions so everyone knows that we are keeping a very close look at the area... Oh and of course, keep improving our already good relationship with all the other powers while increasing our own economic and military strength...
Well there are actually many other things we can still do to try to discourage the PRC from getting within our EEZ.. Formally allying with the US might perhaps be one of them, but that doesn't seem to help much in the case of the Phillipines.. and neither is the FPDA much help to the Malaysians in this case too... So unless there are strong indications of PRC going the Imperial Japan way, we should not be too hasty in joining an alliance or such..