A self-contained 5-1/4" floppy disk drive with USB.
Software to read or write Apple II (DOS,ProDOS), Commodore, Atari, MS DOS, CP/M, etc using Mac or PC.
Options: Built-in emulators, protected disk copy, disk duplication, disk repair, integration with online archives (asimov, virtual apple, etc.), desktop disk mounting, etc
Any thoughts?
Has it been done?
Who wants to make it? 
I'm not entirely sure I follow what your objectives are. Is it like any of these things:
http://www.thesvd.com/svd/apple.php
http://www.spvhd.org/
http://dreher.net/?s=projects/CFforAppleII&c=projects/CFforAppleII/main.php
All have USB components, all do image hosting/archiving/mounting in some form, etc.
David,
I think what he is talking about is 5.25 drive that can be plugged into a USB port on a Mac/PC and then used to copy old Apple II, etc software directly to the new computer as a disk image. At least that's what I gathered from what he said.
Oh, ok - then he means one of these:
http://www.willegal.net/appleii/appleii-disk-int.htm
Sort of like that last reply's project, but for many different disk formats, self-contained and well, a finished product.
That project's last entry was almost 4 years ago and it still appeared unfinished.
It just seems kind of silly that there's no turn-key solution available in 2013 for reading and writing legacy disks.
Not enough demand I guess.
Reading is one thing, writing is quite another since there were different methods (GCR, MFM, etc.) and formats.
http://www.deviceside.com/
http://www.kryoflux.com/
Are there any that use an SIO port so I can use it with my Atari?
Sounds like:
http://afs.atari.org/sio2sd.htm
Exactly so. It's (much) more difficult than one might imagine, especially for some of the things that were cavalierly tossed in - "copy protection," "desktop mounting," etc. And, demand wanes with each passing year - and more and more disks become unreadable.
Solutions exist for much of what you asked about, save for (automatic) Apple II copy protection duplication. But they tend to be point solutions, as opposed to an all-in-one device.
Get your soldering iron out...