Both Davids' responses do a good job of hitting the "big picture culture conflict" side (Poepoe) and the "little picture fix" side (Howery) I was basically going to say the same general things, but lean toward the agent issue as a realistic improvement which might have actually done a lot of good. Howery's observation about the churches is also astute. There was often considerable conflict between the government agents and missionaries operating on the reservations, and based on my profesional research the missionaries were invariably much more interested in the physical and cultural well-being of the people on the reservations than the Indian Agents. For most low-level US government bureaucrats, getting assigned as an Indian Agent out west was like going to Siberia - it typically only attracted the laziest and most corrupt people.
A broader problem is that the US government never fully decided what it wanted from its reservation system. At first (in the early-mid 19th century) reservations in the west (although they weren't always called that at the time) were established just to relocate Indians who had become "inconvenient" in their original homes. The reservations were large and typically contained enough resources to sustain the tribes' aboriginal farming or hunting/gathering practices. There was really no concerted US government policy to acculturate them as there was no thought they would ever become US Citizens. After the Civil War, and thru the late 19th century, as conflicts arose between settlers and western tribes, reservations became essentially prisons where the policy shifted to forced acculturation. Traditional subsistence patterns were banned and most children were put in government run boarding schools to be taught English and "white" culture. Church run boarding schools were also tolerated on reservations, but many were closed because the missonaries proved to willing to tolerate and support traditional language and cultural traditions. Yet, Reservation Indians as a unit were still not considered US citizens. Although not deliberate "genocide" , it was expected that Native populations would gradually disappear from a combination of low birth rates, adoption of Indian children by whites, intermarriage, and acculturation ("The Vanishing American"). However, Indians neither vanished nor was the US government really willing to spend the effort to fully and affcetively acculturate them. It wasn't until the 1920's that all indians became US citizens (and citizens of the states within which they reside). Also in the early 20th century, most tribes lost all formally recognized self-government. In the 1970's the trend has reversed, and most tribes are again recognized as dependent sovereign nations within the US, creating the fascinating mix of overlapping state, tribal, and federal laws we in the west deal with on a regular basis. Many Indians I know are proud of both their tribal and US citizenship (Indians have a tremendous record in the US military, for instance), but are much less willing to recognize State authority.