Not that much simpler; we end up abandoning a simple tree structure and end up building a web when we have to start including horizontal gene transfer.
Quite. — a similar problem is also one of historical linguistics where a simple tree structure of “descendants” is often inadequate.
I find all of this classification for it's own sake to be a wanting approach that bares little fruit in terms of inference, and mostly seems to exist simply because it comforts the minds of men to classify, even when it can obviously not be done.
Even ignoring horizontal gene transfer, the Neanderthal man is typically considered a separate species from the modern human, yet it seems almost inescapable at this point that at least significant populations of the latter have some horizontal ancestry of the former, but some populations also lack it.
