It increases the cost of all menu interactions with non-focused app by one click. I'm not sure if gnome 3 duplicates that menu bar on each monitor, but if it doesn't then it means significantly more steps (strictly speaking) to locate the app, locate the menu bar, return to the app.

It also encourages a poor menu paradigm (imo) of nested menus. Iconography, ribbons, searchable action bars, and other innovations are more often found on OSes where the choice isn't made for the user.

It seems really silly with how UIs have evolved to use a Mac at work, with half of the menus in the app and a seemingly random other half in a disconnected set of nested menus. That's my experience at least.

Focus follows mouse breaks if you need to move the mouse away from the window over other windows to the top bar.

Focus follows mouse is an extremely useful feature which allows you to move focus without changing the relative arrangement of windows to each other (whereas Alt+Tab or relatives would bring the selected window to the front).

Additionally, a top-level menu bar is always there and requires a horizontal layout (I think?). In a window, each application can decide to hide the menu bar at will with only a vertical panel being visible at all time in all apps.

For a UI consistency is better than dynamic elements. In fairness this can be used as an argument in favor of the global menu too, depending on exactly what you want to be consistent.

Linux desktops are usually "focus follows mouse" (because the scrollwheel is part of the mouse not the keyboard), so in the second screenshot with two apps side by side and the right one in focus, moving the mouse to the menu will result in the active application and menu changing.