One of the cool things they've taken the trouble to do is to make sure that almost all functionality is accessible from the command line.
As such WEKA is easily scriptable. This is great for integration into bigger projects. It can easily be chained like standard unix tools; I've used this functionality in projects with good success.
What I'm saying is that to use command-line machine learning, I would have to couch it in a bunch of scripting. At that point in time, I might as well use library bindings. So command-line is not a selling point for me.
