>> We are barely able to trace our individual ancestors back more than 2,000 years.
Nobody can reliably trace their ancestors back 2,000 years. For almost everyone, going back more than 500 years is nearly inmpossible.
>> Homo sapiens in their present form have been around for at least a million years...
Homo Erectus was, and we might descend from them. But anatomically modern humans came around more recently -- maybe 200,000 years ago or a little more.
>> So that leaves a big gap of unknown, that people tend to fill with fable and speculation.
I know of almost nobody who fills the gap between 500 years ago and 200,000 years ago with fable and speculation. Rather, the speculation is filling the gap from 100-200 years ago back to 500 years ago, when they can finally claim some noble or another that they descend from.
>> There is no evidence that humans sprang from a single group, but more likely a mixture of groups, even today people show traces of neanderthal genes, indicating that they did not become extinct, but rather an amalgamate of several types.
You need another adjective. There is lots of evidence that all living members of our species descend from the same ancestors not too far in our past. But if you look at ancient human specimans, you would have to go back much farther to find a common ancestor. For instance, because it is now known that anatomically modern humans interbred with Neanderthals, so we are (arguably) of the same species, you would have to go back much farther in time to find a common ancestor between yourself and some ancient Neanderthal specimen.
>> Our recorded history is but a minuscule fraction of the story of humanity
That is true. There were huge populations of humans that we know almost nothing about. 20,000 years ago, the genetic diversity of humans was as broad as it is today, but along totally different clines of variation. The history of humanity is not a tree but rather a story of constant migration an intermingling, followed by isolation into genetically distinct population groups, followed by further migration and intermingling. Throwing another wrench in -- sometimes cultures would only adopt the language or customs of their neighbors without becoming genetically intermingled. Archaeogenetics, anthropology, and archaeology are a fascinating collection of fields.
I recommend David Reich's book Who We Are And How We Got Here if you like this stuff.