Kukulza, it's not a question of incriminating once more the Japanese or the Kuomintang for all the problems -- or saying that the Japanese were looking for the 'good savages', as you imply. The situation in the island was and is still far from being that manichean/simple. The aborigines simply wanted to be respected as what they are. It is the same today, as they want to be treated in a fair way like everybody else.
The issue is that since the beginning of the history of Taiwan, around the 17th century, when the island became chartered on the maps, the Han Taiwanese settlers and the aborigines didn't get along. The two communities are still having very different characters/situations today.
When the island was under the Dutch colonial power, the Aborigines were the closest ally of the Dutch and were fighting along them to crush all the revolts of the Han migrants that had came from China to work on the agricultural lands.
Finally, the Han migrants mixed with the plain tribes, but the tensions remained with the mountain tribes. Because of this mixing, 80% of today Han Taiwanese have at various degrees some aboriginal blood, but it is something that they ignore. They don't want to know or even recognize this fact when they are told about it, because most of the time they simply despise aborigines -- even today.
In the 19th, when the camphor and wood industry encroached on the traditional territory of the mountain tribes, Han militias were set up to hunt down aborigines. When the Japanese arrived in 1895, the Aborigines first fought them as you underlined, but then they accepted their rule, seeing it as a way to become real citizens equal to the other and not a 'game' to hunt down.
Today, many aborigines are still siding with the main political force, mostly the Kuomintang, because that's were they think they find a better protection. And for the aborigines that have lost their illusion with all the political movements in Taiwan, they look towards another power. A Truku leader fighting for tribal autonomy told me once that they have often received promises of autonomy from the Taiwanese authorities, but with no results. So now he is looking towards China where, he thinks, the minorities in Southern provinces already enjoy political autonomy.
Don't forget, Kukulza, that the aborigines situation in Taiwanese society today is far from the Taiwanese dream: their life expectancy is 20 years less than the average in the island; when they have a job, it's often the less qualified and the worst paid. They have poor access to medical treatment, are suffering from alcohol, all kind of abuses, are often the target of (taiwanese) developpers trying to steal their land. Very often, the families have exploded with the parents working in the cities when the children are left in the mountain villages with their grand parents... Still today, even if it's changing slowly, many aborigines are ashamed of their origin, often trying to hide it -- I have quite few examples among people around me.
Discrimination ? At least, the government consideres that they are discriminated, as there is an official program of positive discrimination to give aborigines some priority access to job in the administration, school and university system, police, army...
Sorry if I bothered anybody with this long post that is from very, very far linked with ethnic blades. But anyway i made up my point.
If the moderators wish to delete this post, I would understand.
Best
Nicolas