Were the Europeans "more civilized"? Or were they more "developed what advantages the Europeans seemed to have compared to the natives, and why?
Theoretically you can say that a civilized community is one with rules, regulations, amenities, share points, information system, principles and commonalities.
Based on this description, no group was more civilized than the other within their territory. Both the Europeans and the natives, in their own turfs, had their own systems of government, their rules, their own regulations, their own standards of living, and their own system of limitation.
The Europeans never came to a place where there was no organization. In fact, they always met with groups who had leaders, and each tribe had normative ways of life. What the Europeans did not like was that they were different, and they felt that they needed to colonize what they deemed as "savages", and impose their own way of life on them, and especially to spread their religious beliefs.
Surely you may find an argument to this, saying that the Europeans were more civilized in terms of the technology, weaponry, lifestyle, economical system, trade system, and way systems that they had in place at the time of colonization, but communities work with what they have and make the best of it. The Natives never needed any of the "civilized" ways of the European, nor vice versa. Each group was completely civilized within their own idiosyncrasy.