I think the desktop designers should have made a fixed set of top level menus. Only show the non-empty ones, but at least make everyone put apps in them. I'd propose a set including: games, programming, engineering, design, media, office, entertainment, audio-visual, system tools.
I'd also suggest subcategories particularly for games. If there is only one category, or not that many programs total, it could omit the subcategary level when showing that menu.
Put users first and stop sticking your company names in their menus. Add a little structure and some reasonable heuristics. Done.
I think Linux distros could do this since they have packaging guidelines and huge software repositories.