They didn't learn anything from the Yuan? granted I know important the Borjigin legacy was important to Qing rulers, but still if a racially discriminating system didn't work after being established by of the most powerful states in it's day. What made them think it would work then?
It's not as easy as that, obviously - you had conservatives within the Manchus (within the Eight Banners, for examples) which would have vigorously opposed any attempt at Sinification as a threat to their identity - which was why the 'Willow Wall' that banned Han migration to Manchuria was maintained for so long until Russia culturally annexed a large chunk of it.
The Yuan system and the Manchu system were fundamentally different systems, and it's a bit disingenuous to see them as the same thing. In the Yuan, Han were explicitly the lowest caste and were barred from holding positions of significance, as well as subject to a myriad of controls. In the Qing, Han were
not barred from such positions - it was more 'affirmative action' for Manchus.
Similarly I don't think the 'rejected by 99% of the Chinese population' holds for the Qing. Now obviously we don't have opinion polls but up until the 1911 Revolution we don't see indications that a vast majority of Chinese people rejected the Qing. The Taiping Rebellion met vigorous resistance from traditional Chinese as much as from the Manchus, as did the much-less atypical Nien Rebellions. European and Japanese attacks on China were continuously marred by resistance from the local Chinese. The Qing Empire, even to the end, could count on the services of very notable Chinese leaders such as Zeng Guofan and Li Hongzhang (to mention a few), and even revolutionaries such as Liang Qichao advocated keeping a Qing constitutional monarchy in place to keep the peace in China. It is also important to note that the Qing fell in 1911 because local power brokers (esp. Yuan Shikai) saw little benefit in sticking with the Qing any longer and declared independence - and not because they were infatuated with Sun Yat-Sen's nationalism, as would be shown in the anarchy after 1911. I really do think this 'Manchus were foreign' aspect has been vastly played up by the histories, esp. Chinese histories which obviously have a dog in this fight. The Chinese, for the most part and whatever their ideal preferences, were tolerant of Manchu rule.
In any case, Qing ethnic 'otherness' was an integral part of their Empire's administration. The fact that the Qing were not Chinese meant that they could be all things to all people - they could be pious Buddhist Khagans in front of the Mongols, they could have Hui and Uighur imams invoke their name when praying to Allah, they could implore Tibetan lamas about the secrets to Nirvana in Tibet, learn to play the spinet in front of Westerners and yes, they would pray to the Rain Gods at the Temple of Heaven in front of the Han. With every ethnicity they came across, the Manchu tried hard to adopt the trappings of the conquered culture without being bound by them.
This seemingly-schizophrenic identity was not something that the monocultural Chinese view of the world would never easily accept (one of the reasons why Chinese history is not more impressed with the Sung Dynasty), and it was why the Qing were so much more successful at creating a multi-cultural Empire - and maintaining it for 300 years at that - than almost every other nomadic tribe before them.