Apologies if I'm overlooking an option, but...
I use a customized TrackInfo display as my Playing Now screen. It shows all kinds of useful info from my customzed MC music database.
And, I've upgraded MC many times (every version since Media Jukebox 3). At this step, MC automatically grabs lots of settings and info from the prior version and applies them to the new version.
But, left behind is my custom TrackInfo, and probably any visualization customizations. So I have to dig into Windows, find the folders, and copy over my customized html and css files into new MC tree, then open MC and select my Visualization for use. Not a huge problem, but perhaps it could be automated if MC had a slight tweak to recognize and handle user customized files.
In a development platform I use, Drupal, there's implicit way to mix standard and custom app files (code, HTML, CSS, whatever). In addition to standard folders and files, Drupal also creates a specific folder that is empty, intended to be where the user can put customized versions of certain files. Drupal automatically first checks the custom-files folder and uses anything there, then looks in its standard folders for whatever else it needs. Therefore, if a user-customized file exists it overrides the standard file. But because this override ability is normal behavior using "official" folders, nothing is hacked or lost. Therefore, when a new version comes along, it is simple for the upgrade process to automatically copy any user-custom folder tree/files into the same location in the new version.
I realize that if MC has to constantly check in two places that's not so good, but same with Drupal, which remembers that it found custom files so it is not constantly thrashing around. Just a thought...