I've been working on a timeline on this as I am part aboriginal and would like to see how history plays out with a non-Chinese Taiwan. I haven't gotten very far though. I have considered the Kingdom of Middag but there are very few English references and the wikipedia page does not have any sources.
The major issue with uniting the aborigines is the fact that there were almost thirty tribes, each with a different language and culture. Many of them were in constant war with each other as well. Devolved's idea of the Dutch providing a unifying force is very good, however, we then run into the second major problem. Taiwan was not fully "conquered" until the Japanese came with modern weapons and aircraft. The island is simply too mountainous to be able to control with 19th century technology. The Dutch could probably get a unified colony on the western plains and possibly, though unlikely, the eastern plains, but control over the mountains would be tenuous at best.
As for why they got taken over by Han migrants so quickly, the answer is that the plains tribes found it easier to merge with the migrants rather than face discrimination and increased taxes under the Qing. Han culture has a long history of eating any cultures it touches (for instance, the Manchus) and becoming the culture of the neighboring societies. Many plains tribe members adopted Han names. As a result, the population of Taiwan grew much faster than immigration from the mainland would provide. Many older Taiwanese families have ancestor records that simply do not extend back to China, as their lineage was the result of a aboriginal ancestor changing his name. One of the greatest myths implemented by the KMT is that the wave of Han Chinese simply pushed the aborigines into the mountains, where they became the current tribes. Not only does this completely marginalize the importance the plains tribes played in the history of Taiwan, but it also disregards the fact that populations in Fujian where most migrants originated did not suddenly suffer a decline when the Taiwanese population grew rapidly.
The Siraya tribe, which had the most dealings with outsiders, had very strict marriage and pregancy laws, resulting in a population much smaller than would be expected. I don't know if other tribes practiced this, but it would be an explanation for why the population was so low.Many of the tribes were/are also matriarchal, with the elder women deciding who marries who. The village matriarchs may well have decided that the strange foreigners with their shiny metal objects and nice clothes were more suitable for their daughters. Remember, most Chinese migrants were male. Once married into Han society, the children's ties to their maternal culture is essentially cut off.
Their technological knowledge was also not as developed as one would think: the most important objects taken during raids on Chinese settlements other than heads were metal implements which implies that either there was a lack of metal ore or that they simply didn't know how to smelt iron. Pa dutch is correct in that most of the ingredients for a much larger and influential culture were present on Taiwan.