If you read the answers people give to the question of what flaws are present in the theory of evolution, those answers generally reflect perceived flaws in the fact of evolution instead.
Evolution, after all, is both a fact as well as a theory. The evidence showing that all life on Earth has changed over time and change over time is the best definition of evolution – is really beyond dispute. Fossils found in very old rocks show different forms of life than what we see around us now. The amount of diversity of life has increased over time as well. All of that, along with evidence found in DNA, the biogeography of organisms and so many other things show that all life on Earth necessarily shares a single common ancestor.
That’s the fact of evolution.
The Theory of Evolution is the proposal for how and why that evolution took place. That theory is based primarily on the work of Charles Darwin and others over the last 150 years.
Most people argue with the fact but never talk about the theory. They say that evolution has not taken place. They don’t talk about natural selection which is the aspect of the theory that required true genius.
Other things in science are both a fact and a theory. Most recently Global Warming could be described that way.
One the one hand, it is a fact that the Earth is warming up. Glaciers are melting. As a result water levels are rising. Average temperatures are rising. All of this is a fact. No one can really dispute it.
The theory is that this warming is due partially or completely to human activities, primarily the release of greenhouse gases.
The theory can be debated but the fact cannot.
The same is true of evolution.
The Theory of Evolution has changed quite a bit since Darwin first explained it in his book “The Origin of Species”. Darwin was a contemporary of Mendel, but was not aware of Mendel’s work so he knew nothing about how genetics worked. Genetics are the key to evolution. Now that we understand DNA and have even sequenced the DNA of many different species we understand and can see evolution and confirm the theory more and more all of the time.
As we start the 21st century, there are really no significant flaws in the theory of evolution. It is true enough that we cannot necessarily assign with complete certainty the correct relationship of every transitional fossil to every other one. Occasionally we are surprised by a fossil find. The recent discovery of the fossils of some very small hominids (called “Hobbits”) on the Island of Flores surprised everyone. But the theory of evolution provides high level explanations for everything that we see, even if there is the occasional unexpected find here and there.
Both the fact and the theory of evolution are just fine, thank you very much. Though perhaps the word “flawless” is a just a bit too strong, no one should expect any significant changes in the fundamentals of the theory any time soon.