Watch folders should be able to also watch and encode from subfolders. Having all footage in one folder or having to create multiple watch folders is very inefficient and impractical when dealing with a lot of footage.
I would also like to be able to use Media Encoder to automatically render small HEVC backup files of all new footage to be sent to offsite backup. Setting my whole video project directory as a watch folder with subfolders would allow this; the output folder would be easy to back up.