It would be nice if we could combine different standalone folders in just one. A game with 10 levels can easily take up 10Gb on the harddrive, and it is especially annoying if you want to upload your game to your server... A waste of storage, because there are a lot of duplicate files. Maybe standalone-specific files would have a suffix with the name of the executable file and for the others there is just one copy?
Also I noticed that unnecessary files are copied over, like the audio of
The big escape. That's not a big deal, though, just mentioning it.