I've just recently also talked about this with Jiaz.
My approach would be different:
Looking at other applications like "Telegram", they're using a different default download directory e.g.:
Code:
[DefaultOSDownloadPath]\Telegram Desktop
Now if JDownloader was doing the same, that would already be better.
This means that even if you were to have hundrets of loose files, you wouldn't cause a huge chaos in your general download folder.
E.g.:
Code:
[DefaultOSDownloadPath]\JDownloader\HundretsOfFilesHere
Then, one step further, make sure that by default only multi-item packages are put into a subfolder by default and it should be fine for most of all users.