I think the evolution of flight is one of the clearest examples that the standard theories of evolution purely by mutation and natural selection are still lacking explanatory power. I understand that the theory of Common Descent has ample evidence but let’s not conflate that with the other theories (about HOW genetic drift happens in macroevolution) and turn “evolution” into a religion in our quest to replace creationist accounts. It is a catch-all umbrella term to describe many theories, from “punctuated equilibria” to the “modern synthesis”, which still are in their infancy as the luminiferous aether or phlogiston as physical theories.
I find there is too much suppression of dissenting views in evolutionary and climate science, for my taste. I am talking about universities and publishers taking concerted political action against what is perceived as going against the current establishment.
A new scientific truth does not triumph by convincing its opponents and making them see the light, but rather because its opponents eventually die, and a new generation grows up that is familiar with it. - Max Planck
In many circles, publishing anything critical on scientific grounds is like publicly criticizing capitalism in USA or Islam in Saudi Arabia. A lot of time you get instant downvotes and hostile responses from laypeople.
If you’re curious what I’m talking about, here is probably one of the better treatments of the mathematics behind current theories, for example: