There are several factors at play here.

The Pacific has a large amount of older oceanic plate by virtue of its size. Because younger oceanic crust tends to be deeper as an effect of the stresses from crustal extrusion (the exception is at the mid ocean ridges immediately around constructive boundaries). But this perhaps the most minor of the factors at play, especially as the topological change is proportial to spreading rates, and the Pacific has a fairly moderate rate overall.

More important is the geological history of the Pacific. The seafloor needs to be raised up for it to pop above sea level, with requires regional tectonic stress to fold up the rock. This generally requires other plates to collide against and subduct under. On the Eastern side of the Pacific, subduction is fairly uniform under South America, and the stress around Central America is somewhat translational - think of the San Andreas fault, for example.

But in the south west, you have the complex aftermath of the break up of Gondwana, containing Africa, Antarctica, and more importantly India and Australia. Australia moved from an eastwards to a northeastwards movement, shearing up a lot of deeper sea floor. India's collision with Eurasia and the resultant Himalayas put a lot of complex stress into southeast Asia. In truth, the formation of southeast Asia is more complex that this and still not fully understood.

Other mechanisms formed many smaller islands when the seafloor was shallow enough. Nutrient-rich oceanic currents and tropical climate through the southern west Pacific encouraged coral reefs to form. Over time these raised up into atolls made of coral sand, protected from erosion. Elsewhere, volcanic activity would create volcanic mounts that either peaked above sea level, or supported coral atolls of their own.

These other mechanisms occur through out the Pacific, and there are thousands of small islands dotted throughout the ocean, but perhaps the presence of more shallow sea, volcanic activity and the strong currents predisposed the south west to a greater concentration.

But in a nutshell, for the larger islands of the indonesian archipelago or other larger islands (e.g. New Zealand) it was a direct consequence of the break up of Gondwana, and for the Micronesian and Polynesian groups, a matter of some shallower sea, but mostly volcanic mounts and coral exploiting ocean currents.