I'm going to be crazy, I want to change my phpMyAdmin version 4.4 to metro 2.3 theme. Theme is working but it isn't default, I also added the following line to my phpMyAdmin config file:
$cfg['ThemeDefault'] = 'metro';
It appears that this has either been fixed or was the result of existing cookies in our browsers. The way the ThemeDefault value is implemented causes the user preference (when set previously by a user and stored in the browser cookies) to take priority over ThemeDefault (which makes sense, as it's a default and the user has indicated a desire to change the defaults). The best way to test this is to remove the specific browser cookies relating to phpMyAdmin.
This appears to be a regression in phpMyAdmin; I tested it myself and it didn't seem to work correctly. I've opened a ticket at https://github.com/phpmyadmin/phpmyadmin/issues/12390 where you can track progress.