I jumped to the last couple paragraphs of that piece as most of it appears to be issues that do not have proofs within the theory of evolution. Assuming these issues are presented truthfully, they are valid and should be addressed. If they cannot be addressed within the evolutionary framework this does indeed mean an alternate theory is needed.

The author's alternate theory is that "the basic laws of physics have been designed to generate a cosmos adapted for life as it exists on earth." This theory is not falsifiable. It does not provide any insight into why things are the way they are, while evolution provides incredible insight. I see zero reason to believe this work is anything but ideological.