I'm not sure where you are getting a lot of this. Most of what happened to the Amerind populations was a simple historical accident that could have easily gone the other way. See Charles C. Mann's 1491 for an overview. Some specifics inline:
An outcome that was near inevitable, regardless of if the Spanish came or not.
Europe, Africa, and Asia, all had their share of plagues over the centuries and millennia. This left them far more immune to disease than those on the American continent.
Studies of Amerind immune system genetics suggest that parasites were a bigger issue for them than zoonotic diseases, so it is not surprising that their immune systems were not tuned for this kind of assault. That doesn't make them inferior, just adapted to a different environment that changed suddenly.
Having access to beasts of burden, more easily accessible coal and oil, and other benefits of the geography and wildlife, meant they would advance more quickly in technology.
Claims of technological inferiority of the kind promoted by determinists like Jared Diamond may be somewhat biased because Amerind technology was quite different from Eurasian. For example, the Inka had the wheel but never used it for transportation because of the topography - they only used it for children's toys(!) They also had metallurgy but didn't use it for military purposes - they used it for decoration of public spaces, sometimes on a large scale. They had writing, zero. place-valued arithmetic, better/healthier agriculture, massive public buildings, better public sanitation (see the conquistadors' own writings if you don't believe me), poetry, and philosophy comparable to Greece. Modern population estimates are that Mexico City was larger than any city in Spain at the time.
One possible option for the American natives to have changed this was the possibility to domesticate a kind of horse or other large animals found in the area. Evidence shows they were hunted to extinction instead of being domesticated and used for beasts of burden.
This is controversial. Yes it happened a lot in other locales (e.g., Australia), but there is a fair bit of evidence that the American version was climatic. Plus the evidence from Andean coastal valleys strongly suggests that the population of the Americas happened much earlier than the extinction events.
Some tribes trained dogs to carry light loads, help with hunting, and as animals for battle. This was not unique to the Americas and therefore not an advantage to them when people from far off places came. People from far off places carrying metal swords and armor, and unfamiliar diseases, against people with wooden weapons and weak immune systems.
The population crash from disease killed 50% of the population and triggered a civil war among the Inka, which was the only reason Pizzaro succeeded. Despite his weapons and their population losses, the Inka fought an impressive rearguard action for decades. Oh and European guns at the time were barely functional and were pretty much on par with Amerin longbows in terms of penetration power (even against light armour.)
Oh, and the habits of some tribes to sacrifice the strongest among them to their gods didn't help in keeping a healthy gene pool.
European warfare actually had a higher death toll than the Aztec sacrificial body count. Both tended to take out "the strongest" so I don't see this at all.
There are many instances of Europeans coming to the Americas to find abandoned villages. They found empty homes and fields of crops left growing in the wild because the natives died from disease, long before the Europeans came, or wiped out from wars with neighboring tribes. Like it or not many of these cultures were hanging on by a thread. Anyone that came along would disrupt these fragile societies and bring them down. When unfamiliar cultures meet there will be conflict, and such conflict usually favors one far more than the other.
Any culture is "fragile" in the face of 95% population loss. I forget the references, but even 50% has been known to cause destabilisation and collapse in Eurasia.
