The only downside that I've found to Pop!_OS is the default use of Flatpaks. While Flatpaks are generally pretty great, they can sometimes cause odd issues with interactivity with other apps because of their isolated nature. A pretty famous issue is with KeePassXC's Firefox add-on not being able to detect the Flatpak version of KeePassXC, but there are quite a few other notable examples. I also personally like theming my system icons which is a bit of a pain with Flatpaks.