Well, FAT is what most USB sticks come pre-formatted as, as far as I'm
aware. So the filename restrictions are a problem that a lot of people
are going to face, and not one that we can do much about in Ubuntu.

If you want to back up an entire system, I suggest you put the files
into some sort of archive, and give that a dull, boring name that works
anywhere. A Zip archive is good for cross-platform, or a Gzipped Tar
archive is a more traditional Unix-ey solution.

While I agree that 4GiB maximum file size (note that that's for one
file, not a whole disk) might be starting to limit some people, nothing
springs to mind that would normally exceed that limit (Ubuntu DVD images
are about 3.3 GiB). I suspect that before files of that size become
common, the standard for USB sticks will have changed--probably to NTFS.

You can of course format your stick as NTFS already--that supports
extended filenames, and will work with modern Linux and Windows. I don't
know about Macs.

If you do want to set up the ext3 based system you described, then you
will need to make a small FAT (or NTFS) partition on your USB drive, and
place in there the installer for the Windows ext IFS driver, which can
be found at http://www.fs-driver.org/

-- 
Not ext2/ext3 drivers for other operating systems available when you format an 
external HDD or USB stick
https://bugs.launchpad.net/bugs/237575
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