For me using a product like PrinceXML gave me the power of HTML/CSS to control the eBook's appearance more precisely. Also, using a Ruby-based build process let me take advantage of source control, ERB/Ruby code and other things. In other words, it made the whole process easier to manage for producing a large document.
The only real advantage that I can see to going with publican or asciidoc is that they're free tools. The main disadvantage is that you'd have to define formatting via XSL.