The desktop layout is not as modifiable as some other options, and certain settings require additional software (such as Gnome Tweak Tool) to reasonably modify.

An extension has to be installed to get tray support.

Said a million times already by the other cons but the design is for tablets, even though the primary usecase is on laptops.

GNOME sometimes reduces the whole interface to the absolute minimum, a few examples:

• GNOME hides many advanced options/settings in its interfaces
• Toolbars can't be edited without external tools
• Menubars have been removed in favor of a hamburger menu
• Newer GTK versions remove icons inside popupmenus and menu mnemonics