So what you're saying is that the Natives will only ever be europes punching bag? That's sad. Is there any way to avoid it.
I'll put it this way. The initial contact, in almost any scenario, is going to have apocalyptic aspects.
And it is very unlikely Europe won't exploit the situation.
From there, however, if you have the groups that OTL resisted the longest on a level where they can do that even better than OTL you can get bits and pieces of "pre European societies" coming back.
Look at what 9 Fanged Hummingbird has to say in that regard (the native societies).
So I think the best case scenario is one where a lot of really awful shit happens, but where the societies that manage to avoid the initial wave manage to rebuild something - which may or may not latter suffer imperialism, but by that point we're looking at how India fared, not OTL North America.
But I don't think it is possible to create a scenario where Europeans fail completely in the New World - even if Cortez falls over board, you have a lot of people who will see the Aztecs as worth exploiting.
That's probably a step up for your hoped-for-scenario compared to OTL's "eliminating", though.
I do think Flubber is right that you should read the threads on this before. A lot of the main issues have been covered in depth in previous threads, so while new research is awesome, the basic stuff presented here hasn't yet been challenged - or at least no one has used this thread to mention it.