I used to work at Wolfram Research and directly interacted with SW on a project he took personal interest in, so I feel a bit more qualified than most to answer this. Stephen is without doubt a brilliant mind, and the way he thinks, his attention to detail, and his broad vision of computing are unique in their depth and philosophical impact.
However, his seminal work titled A New Kind Of Science is frequently critiqued as unscientific in its exposition of its core theories. Other scientific works of SW are similarly criticized for bypassing scientific peer-review and offering little substantive theory. I won't comment further on this so you can form your own opinion.
At the end of the day, say what you want about his theories - he is a wonderful, nurturing man who set me on the course to what I am doing today. He gave me my first programming job and allocated valuable time of the brilliant minds at Wolfram Research toward making even the interns productive and excited to work there. His son Christopher is a mirror of his brilliance and will certainly be making significant contributions to science in his own time.
5 years after I left WR, I received his latest book in the mail with a simple handwritten note - "Is this relevant to what you're working on?". It was. I cherish the man and his mind, despite any criticism directed at his work.
As the "Wolfram Derangement Syndrome" alludes, he has a very unique style, not unlike our President. And as in that case, it's probably a trap to critique that style and better to simply critique the ideas.
