The counter-argument to the limitations of natural selection does not seem to make sense! Any ideas?

You are forgetting that mutations cause the development of new genetic traits. If the mutation is positive, the new trait will start to out-compete the original, until the old one disappears or is greatly reduced in number. If the mutation is negative, it will start to die out. If the mutation is neutral, it will coexist with the old trait, and in the end, it may lead to a new species through further development.