I recently did this with a large photo collection, and I recommend you stay with Shotwell for this. You have to use a few tricks to get what you want though.
First, make sure you set 'Write tags, titles and other metadata to photo files' in Shotwell, like in @Paradiesstaub's comment.
If the folder names are to be used for tagging, say like 'New Year's Eve', then import folders individually and tag that batch, they'll be listed as 'Last Import' at the top left of the Shotwell window.
Once you get all your folders imported, tag everyone. Once you have everything tagged, it's already written to the individual files. You can move them around and the tags stay.
At this point, you can leave the files in the original folders, or have Shotwell organise them. I chose to have Shotwell organise them by Year and Month sub-folders. To do this, I selected all the files, and exported them from Shotwell to a backup drive. Then, I deleted everything from Shotwell, and re-imported from the backup drive. Now I just import and tag new ones as I go, and Shotwell watches the directory and keeps it organised.
Best Answer
You have to do two things to achieve your four goals.
First, don't use Shotwell to import new photos. Import them with Nautilus to wherever you want to keep the pictures.
Second, change a setting in Shotwell. Edit/Preferences/Library(tab)/Import photos to: and select 'Other', then navigate to where you store your photos. This should be a drive that mounts automatically whenever you login. Check the box 'Watch library directory for new files'. That will automatically detect changes as you add or subtract images using Nautilus. The 'Importing' settings are irrelevant. You will not be using Shotwell to import images, so no need to change them.