The problem: when upgrading phpMyAdmin on basic shared hosting using FTP, by default there is 19 MB of files to upload!! (And that's just the English version.)
If I look through the code I can see several things that (I think) are optional to upload, such as the "/docs" and "/js/jquery/src" folders. I think all of that stuff should be moved into one folder.
And there is also everything in the lib folder. It seems you can't just remove the stuff you don't want/need. For example I don't care about the PDF or charting plugins, but I need to upload these each time I upgrade PMA.