After so much wait, with the new Exchange Updates released on June 2017, now will be possible to recover item their original folder in Exchange 2016.
However, there are still some limitations:

1. First, to use this functionality, the user’s mailbox must be on a Mailbox server that has CU6 installed. The user must also use Outlook on the web to recover to the original folder; neither Outlook for Windows or Outlook for Mac support this functionality, today.
2. If an item does not have an LAPEID stamped, then the item will be recovered to its folder type origin – Inbox for mail items, Calendar for calendar items, Contacts for contact items, and Tasks for task items. How could an item not have an LAPEID? Well, if the item was deleted before CU1 was installed, it won’t have an LAPEID.
3. And lastly, this feature does not recover deleted folders. It only recovers items to folders that still exist within the user’s mailbox hierarchy. Once a folder is deleted, recovery will be to the folder type origin for that item.

I have not doubt that this will make your life easier and your end-users happier