Hi Sjors, 

the non-GUI usage of Relion has several major advantages, and it would be more than important to keep it available in the future :

-reproducibility : sharing with a colleague a series of commands that lead to successful run takes a second (copy/paste), but if you try asking a GUI user to show you what he precisely did past weeks, it will take him minutes to go through the complicated directory structure and dig out the useful information
-adaptability : re-launching a job that ran days ago by changing one or two parameters takes again a second when not having to go through the GUI
-scriptability : obvious advantage when developing own's processing pipeline
-tracability : a typical non-GUI user will keep every single command launched in some text file, and could therefore provide the entire project protocol at once to reviewers, programmers... I've not seen GUI users able to provide quickly such useful document.
-and maybe most importantly : making the user more active, and increasing it's knowledge. It is true that command line might seem less friendly in a first place to newcomers to the field. However, it forces the user to think a bit more about every option, and see the options not even available through the GUI (set by default, or not accessible at all). It is also a step towards more fluent linux usage, and scripting, which often become a necessity for hard projects. Relion has this great advantage of making good quality image processing available to anyone with no background (which was absolutely not the case 10 years ago, where the learning curve was steep and long), but one should take care of letting the new generation learn a number of basics, which can become crucial when encountering difficult cases.

Cheers
Ambroise