Yeah it's really simple. I didn't realize that the font can actually still be read even on black background.
(But there is also white colored font in the game, so someone might know how to change it.)
I edited all files with a bright background in the Graphics-Pictures folder (Pokemon summarys, Bag menus, Battle windows, etc.).
Just download Waynolt's files and mine and everything should have a dark background.
Pictures.rar
I also included the original files as backups already since there are 31 separate files, so you don't have to make a backup.
In case the contrast in the Bag Menu and the Pokemon summarys isn't good, I also included a little brighter menus.
I hope this helps.