Personally I think it’s better to have just the files themselves in a zip file. This has quite a few benefits:

• Users can just download the zip, and they are ready to start playing!

• The Itch.io app knows how to handle game files and update them efficiently, something it can’t do with setup files.

• Users won’t have to worry if the project comes with an uninstaller that removes all files, or leaves some leftovers.