I'm a huge fan of WebCEO myself, but as others have said, what you choose to do with the data it gives you is down to you and the client. It does automate processes which would be insane to run manually, and can help catch aspects you might have overlooked. For ongoing monitoring and reportage, it does the hard work in the background. But what I do with the help WebCEO gives me is built entirely on the 15 years I spent doing web sites before going professional about SEO.
What I always say to my clients is that SEO is not about rankings, its about revenues. You not using WebCEO or the other software to guarantee a #1 or whatever, you are using it to get them to a position where they are earning more revenue, whether that position is #1 or #20. In that regard WebCEO is particularly good for helping you look at the bigger picture.