Did a clean windows 10 install last week and then imported my GoG folder into GoG Galaxy. After this i had 241 new "GameName [GoG.com]" folders in my StartMenuRoot.
Since the win10 start menu's "all apps" only allows top level folders, flattening any subfolders, i see why gog did this, but i use "classic shell"/"start10" start menu & fences!
So i've written a script that moves all these folders into an "All Progams\GoG.com" folder, plus it extracts the primary shortcut to start the games/expansions and copies them into an adjacent "All Programs\GoG" folder for quick access:

https://gist.github.com/blunet/3e279972233ea934489a

Explanation on how to use : read the first 4 lines of the script.

(And here is one that creates shortcuts for all steam games : https://gist.github.com/blunet/f0e14a3d38ed1c3ba36b)

Nice!
Also remember that Windows 10 cannot have more than 500 items in the menu, or at least that was so two months ago. A problem discovered before the release of the whole OS.

Will keep your script at hand, just in case. Thanks for sharing your work!!

The reason you have a problem is because you have so much installed. Just keep the installers and install what you actually use.