As the MATLAB Report Generator's development manager, I am concerned that this question may leave the wrong impression about the Report Generator's capabilities.
For one thing, the Report Generator does not require you to break a script up into little pieces and run them inside a template. You can do this if you choose and in some circumstances, it makes sense, but it is not a requirement. In fact, many Report Generator applications use a MATLAB script or program to interact with a user, generate data in the MATLAB workspace, and as a final step, generate a report from the workspace data.
Moreover, as of the R2014b version, the MATLAB Report Generator comes with a document generation API, called the DOM API, that allows you to embed document generation statements in a MATLAB program. For example, you can programmatically create a document object, add and format text, paragraphs, tables, images, lists, and subdocuments, and output Microsoft Word, HTML, or PDF output, depending on the output type you select. You can even programmatically fill in the blanks in forms that you create, using Word or an HTML editor.
The API runs on Windows, Linux, and Mac platforms and generates Word and HTML output on all three, without the use of Word. On Windows, it uses Word under the hood to produce PDF output from the Word documents that it generates.
The latest release of the MATLAB Report Generator introduces a PowerPoint API with capabilities similar to the DOM API. If you need to include report generation in your MATLAB application, please don't rule out the MATLAB Report Generator based on past impressions. You may be surprised at just how powerful it has become.