The history of one society/culture conquering, assimilating, subjugating or otherwise treating badly the 'others' that they encounter is not particularly a Canadian problem; it has gone on long before the Romans. Part of the reason for the extent of the social conflict was, for want of a better term, the clash of cultures at different points on the social scale (I hesitate to include the term 'evolutionary'). At the beginning of European contact, it was the age of sail and gunpower meeting largely hunter-gatherer societies, many nomadic. By the time colonization got underway, it was the Industrial Revolution while the indigenous societies were still at the hunter-gatherer stage.
Before colonization, not all was sweetness and light in the Americas. War between societies, genocidal intents and slavery were not uncommon.
There may be a general unhappiness with the Indian Act and the 'reserve system', but I am not aware of any consensus on a better version, on either side. I am most familiar with Northwestern Ontario, where there are approximately 30 remote (fly-in/ice road) FNTs with a total population in the area of 10,000 (my number may be off). Most are under 1000 people (some very under), a few are in the low couple of thousand. That is their traditional territory, but in terms of clustering in fixed houses with electricity, an air strip, store, etc.; i.e. 'living Western', there is no economy to support that, and no potential for one, and no desire to turn back the hunter-gatherer clock. Their only hope for any income beyond government handouts is resource extraction income, and they need to remain proximate to their territory for that. Without an economic base to live like now do, social problems abound. The residual effects of the residential school system, probably made them worse, but they would still exist regardless.
A large number of years ago, there were very informal discussions about coalescing many of these into a small number of larger communities, even very distant from 'Western towns', where there could be a road connection, decent infrastructure, hospital, high school, etc. plus a critical mass for some kind of economic base, would be more achievable. There was no appetite for that, on either side.
The current system is very costly. Simply putting in a water system in a remote community that may only have a few hundred people is a multi-million dollar, multi-year venture. We could give each and every man, woman and child a million dollars, but the social problems would still exist.