Well thats going to be a bit hard for the average bloke in the street. But I can research and look up scientists who show that some of the accepted beliefs are wrong or at least in question. One of those is with how many scientists have come out in recent times and questions darwins tree of life. I could site several prominent science sites that have shown this.
Darwin's Tree of Life May Be More Like a Thicket
New Scientist says Darwin was wrong – Pharyngula
Horizontal gene transfer in evolution: facts and challenges
The problem is for some of the evidence is that its nots so black and white. Like I mentioned with the interpretation of bones and fossils you will have x amount of scientists saying that they believe that it fits in with their view and then have some others that question that and bring up valid points. Even if the majority say it is supportive of a transition because there are some that bring up other possibilities it places doubt over the evidence and at least puts it on some shaky ground to be used as strong evidence.
Because a variation can be within the same species and not a new species. Evolution needs a progressive transition of a creature into another species. So those variations should gradually show changes that turn it into a new shape or type of creature. But this is where it gets hard to tell and where I believe that scientists can misinterpret transitions. Because like you are indicating there can be a stage where you just can tell whether its a variation of the same creature or a transition. Such as with a dog there are many shapes but they are still dogs. Or like I said with bats there are many bats that are classed as different species but they are all still bats with bat shapes. They havnt turned into owls or lizards.
Like I said thats where its hard. But I would have thought if a creature is transforming from one to another completely different shape that there would be some stages in between. Like a Dino to bird. Would you have a stage where the wings are stumps and useless before it got to the point of functional wings. Or do the wings pop out in one generation completely working.
There is still a fair amount of conjecture about what is classed as homo erectus, Neanderthal and homo sapiens. Some say that they are all the same species or at least early homo sapiens fall into the same species as homo erectus and Neanderthals. But as you see from the skulls found at Georgia and my example with dogs you can have a lot of size and shape between the same species. So without any solid evidence such as DNA then its up to interpretation and this is to sketchy.
Even with the DNA evidence it has been showing that there are some similarities that make some of the separate species that scientists had categorized put into the same species. Then we get some connections between totally different shaped creatures who were thought to not be on the same evolutionary line linked together through the DNA. There is also some evidence that the so called different species cross bred and may have produced another so called species that has been labeled a transition. But the main point is that because of all this conjecture its harder to definitely say what the transition for ape to man is or whether they are just apes and humans. There could be one group that is just humans and has a great amount of variation in size and shape and then another group who are apes with great size and variation.
We just dont know definitely because we are looking back like a detective in a cold case and trying to piece things together. But what this also does is put a question mark on some if not many of the so called transitions that are needed to show a gradual transformation of ape to man. We had a number of species that scientists were saying were showing the stages of ape man transforming into a human. Then with the new discoveries they have lost a bunch of species and stages in the line that was showing this progression because they are now lumped as being in the same species with variation. So what happens now to all the gaps that are left with these species taken out. So to say that the evidence is so strong that you can call it fact is to me a little premature.
Homo erectus - CreationWiki, the encyclopedia of creation science
https://theconversation.com/of-heads-and-headlines-can-a-skull-doom-14-human-species-19227
New fossil suggest ancient human ancestors the same species: Homo erectus | Genetic Literacy Project
New DNA Analysis Shows Ancient Humans Interbred with Denisovans - Scientific American
The key issue is the ability correctly to infer a genetic relationship between two species on the basis of a similarity in appearance, at gross and detailed levels of anatomy. Sometimes this approach....can be deceptive, partly because similarity does not necessarily imply an identical genetic heritage: a shark (which is a fish) and a porpoise (which is a mammal) look similar
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BONES OF CONTENTION, 1987, p. 123
There are other scientists who dont consider Australopithecine as ape to human but just ape. It is grossly like an ape and the evidence for it walking is highly contentious.
The Fall of <i>Australopithecus sediba</i>: Controversy and the Quest for Glory Cloud Claims of Human Ancestry - Evolution News & Views
Well when you consider that for every single species that is claimed to ever walk the earth there would be millions. So would it stand to reason that there would be billions of transitionals for each and every one. If mutations are primarily non advantageous and only 1 in 10,000 are beneficial then would there be billions of failed transitions. If a reptile found that wings were advantageous through natural selection they would only find that through a process of trial and error. There is no real intelligence behind evolution and its a blind and random. Though the ultimate aim of natural selection is adaptation to the environment for survival there is still a lot of mutations that will fail and be of no use.
So wouldn't there be many generations of failed changes that were not taken on if it is random and chance. For a reptile to get a wing it may have gone through 10s of thousands of other failed mutation that maybe produces stub toes or hair in places on its body or a change in its skin or a change in its metabolism that all were not advantageous. These all would have nothing to do with wings because it didn't know it needed wing or that wings would have been advantageous in the first place. So any mutation could have occurred in a pot luck process. Then eventually after many non beneficial changes it eventually found that having wings was beneficial for survival such as avoiding predators. So wouldn't there be billions of fossils of failed mutated creatures we would find that are the results of getting the ones we ended up with. Even just for wings we would have to have many stages of wing development to finally get a good set of wings that were beneficial. Would the stages that we non beneficial be rejected anyway as not being advantageous. (Forgive me if I sound a bit simplistic as I dont know much about genetics so this is just my understanding).
If you take the Pakicetus as a transition for early whale which lived on the land. To get from that to a whale would have taken many thousands of attempts. It just didn't find the right things it needed in one generation. There would have been many generations of failed changes that just didn't work because its all based on random chance. Even just with the size factor to go from a small dog like creature to a whale which is near 100 feet and around 170 tonnes would need 100s of stages in transitions. The next generation cannot jump to big in size because the mother would not be able to have the baby. So it would take tiny changes in sizes and that would take hundreds of generations which would leave hundreds of fossils of different sizes to get to the whale. But all we have is patchy stages with fairly big jumps. There is not much evidence for all the other things that need to change like breathing, shape, different tail movement which requires a rotation of the hips and pelvis, hip and pelvis which to me in the process would leave a creature struggling to move as it was gradually changing, sonar and hearing, seeing under water ect. Thats not taking into consideration that some of the features of Pakicetus are also unrelated to whales. They say it adapted to water because it had to eat fish. Yet its teeth were strong for ripping flesh. They say it learnt to be in the water a lot yet its legs were built for fast running across land.
So as you will see there is still a lot of contradictory evidence for transitions and I dont think there is any real qualifications that can determine what a transition is clearly because much of it is up to visual interpretation.The only real way that a line of transition could be shown perhaps is through genetics. But you also have to remember that variation is also shown through genetics so you have to have a clear understanding of what a species is. Especially if you go back in time where its harder to establish because you can always have the DNA and we dont know whether animals cross bred more often to produce new kinds of animals or other forms of HGT were at play.
Digging up a creature that happens to have a few similarities to another and then making a whole line of out this is not a solid foundation as you also have to consider the differences and that there is no other real evidence like genetics to make sure it is a fact. Especially now that genetics is showing that the lines and trees that were made in the past are coming under question. Some creatures are being taken out of those lines because they are related to another totally unrelated line of creature and some creatures are being linked together that show no resemblance yet are closer through genetics than the animals that scientists use to say belonged together. Its still early days so we will have to wait and see. But I dont think you can say that the theory has a strong case to say its fact.