While there are still plenty of things that should be done, some long asked-for features, as well as some other changes, got implemented in MP3 Diags Unstable 1.1.12:
It is now possible to run external tools (like audio players, taggers or whatever you want) by right-clicking on a file name in the main window. See this link for the details (the UI will quite likely change in the future, as I don't like it, but should suffice for now). The same right-click can be used to open the folder containing a file in your default file explorer.
You can apply transformations from a script, without entering the GUI mode. More about this at the bottom of this page.
If you decide that you want to delete some MP3 files, you can do so by pressing DEL in the main window.
I fiddled some more with Gnome 3, with its issue that by default it doesn't show the close buttons that MP3 Diags expects. Here's the current status: I added custom close buttons to the windows that didn't have an "OK" or "Cancel" button, but, since I hate having 2 close buttons next to each other, the custom buttons are usually hidden, and get shown by default if Gnome 3 is detected. Since this detection is far from perfect and given that some distributions show by default window decorations that include a close button, it is possible for the user to hide or show these buttons. There's a checkbox for this in the "others" tab of the Configuration dialog, in the "Misc" section.
Two new transformations have been added: an "APE remover" and a "Non-audio remover". While they are both rather obvious, the latter is described in a little more detail here. Note that they are both hidden by default and to use them you need to make them visible in this window.
One last change is that the quality thresholds for the CLI analyzer are now taken from a session (the last open session if not specified otherwise), rather than using the program's defaults.