The major issue having to do with the Indian Removal Act was whether removing Indians from settled areas and forcing them to move to "Indian Territory" was a good policy for the Indians.
President Jackson and his supporters argued that it was a good policy. They argued that it was sad, but inevitable, that the Indians were going to disappear as they lost out to "civilization." They argued that the only thing to do with them was to get them out of the way of civilization so they could live in their old ways and, perhaps, be gradually civilized by missionaries.
By contrast, some people argued that the Native Americans were already becoming civilized. They pointed to the example of the Cherokee who had a written language and a constitution and who lived as farmers. Some of the Cherokee even had black slaves. Opponents of Indian Removal argued that other tribes would soon civilize themselves using the Cherokee as an example.
Jackson and his side won out and the Native Americans were removed from the Southeast and moved to areas west of the Mississippi.