In Guns, Germs, and Steel by Jared Diamond, why did the different areas of Austronesia develop so differently?

The Austronesian expansion refers to one of the largest population movements of the past 6,000 years, in which people of Taiwan (or, as Diamond states, "stemming ultimately from mainland China") colonized Java and Indonesia.

Diamond suggests that different areas of Austronesia developed differently, stating that the outcomes of the expansion in the New Guinea region were almost opposite to those of the Philippines and Indonesia. In New Guinea, indigenous populations managed to keep "invaders" at bay, while the Philippines and Indonesia saw their indigenous populations wiped out by the new arrivals. 

Diamond chalks this phenomenon up to the differences in cultural circumstances in these areas. New Guinea's indigenous population already had a firm grasp on food production (and were able to successfully accept the introduction of Austronesian pigs, chickens, and dogs), were in possession of polished stone tools, were resistant to tropical diseases, were accomplished seafarers, and had developed trade; Indonesia and the Philippines, on the other hand, were mostly populated by a small group of hunter-gathers who didn't have such honed skills or tools. 

Diamond summarizes this quite effectively near the end of Chapter 17, stating:

In short, the variable outcomes of the Austronesian expansion strikingly illustrate the role of food production in human population movements. Austronesian food-producers migrated into two regions (New Guinea and Indonesia) occupied by resident peoples who were probably related to each other. The residents of Indonesia were still hunter-gatherers, while the residents of New Guinea were already food producers and had developed many of the concomitants of food production (dense populations, disease resistance, more advanced technology, and so on). As a result, while the Austronesian expansion swept away the original Indonesians, it failed to make much headway in the New Guinea region, just as it also failed to make headway against Austroasiatic and Tai-Kadai food producers in tropical Southeast Asia.

In other words, the differences in these indigenous populations' cultural advancements and their ability (or inability) to create a sustainable food source resulted in their respective victory (or defeat) over the colonization efforts of Austronesians.