Twenty years ago, we started decoding the human genome. Nobody thought descent was linear in one "human" line or whatever it is you're trying to say. Try 50 years, maybe more? When Lucy was found, I think she was initially handled as the "missing link", but that notion quickly disappeared when other Australopithecene species were dug up and we were unsure which one of them was our direct ancestor.

Fossils are snapshots of a species at a certain point in time. If a species retains a relatively unchanged form over a long timespan, homo erectus coming to mind as an example, it means they were adequately adapted to the conditions they had to live in for a long time. Heavy physical mutation and speciation typically occur as a response to different selection pressures, aka a change in environment, isolation of a group, filling a different niche in the ecosystem, etc., although not exclusively so. Genetic drift obviously happens aswell.

If we find two specimen in the same layer, meaning from the same timeframe, but they look completely different, we are probably dealing with two different species. Now we have to figure out how far they're removed from their last common ancestor. DNA tests don't really do much here since DNA decays within millenia. No real use trying to get anything from bones that are hundreds of thousands of years old. Fossils aren't bones and they have pretty much no organic material left in them.

The entire human family tree is a work in progress, as with anything in science. As new information comes to light, it is updated. There are always different theories on how to classify species X vs Y and how they relate to one another and new discoveries can and do change the way we see things all the time. We can deduce certain estimates, for example how we are probably descended from homo habilis rather than a representative of the paranthropus group, simply because our bodies look more like the first. Researchers look at details in the skeletal structure such as facial/cranial features, bone density and proportions, joints, teeth, and a million others.