Great Idea for a topic, alot to touch on here!
In regards to the Native aborigines in Canada, those people for the most part had made earlier contact with the explorers from Europe even before parts of the now day United States were even settled. Trade was established and customs developed. There are also some big differences between the two native groups from both countries. For the most part Canadian Natives were not very nomadic and took to settle in an urbanized type fashion, while for the most part Native Americans in the U.S. were nomadic, and changed location based on the wild game they were hunting, or seasonal influences. They also came into contact with the colonists and explorers at a much later time.
Part of the reason in why U.S. Natives seem to have been treated worse was the way in which they were used as leverage and pawns to fit the strategic and leveraged needs of the many European nations that sought to carve up the new world. This did not bid well for the Natives who were constantly deceived, and pitted against many of their old territorial enemy tribes, as welll as old allies. The history of the entangling of alliances that is famous in European history was brought upon these people.
A big part of the downfall of the Native Americans was the rapid development of their people to the sudden change and culture shock they received from the foreign settlers and their new technology. In a sense their tribal culture was bombarded into assimilation until it was hard to distinguish them from their new neighbors. This is unfair, but "curiosity killed the cat" applies to this event. Once the population of the colonists continue to grow and grow, the Native American culture and peoples were all but eradicated from the New World. People forget that the inhabitants of the USA today from the past were all displaced Europeans, who all had their image of the Native Americans. Said to be inferior due to their primitive lifestyle, and they definitely did not forget the many tribes who may have sided with an enemy country, be it England, or France and others.