The problem is that Ubuntu is yet to support MTP natively. I hope with the next version, Ubuntu 13.04 (Raring Ringtail), they will fix this annoying problem. In the meantime, you can manually add MTP support to your Ubuntu installation’s PPA and have seamless access to your Android device.
In Terminal, issue:
sudo add-apt-repository ppa:langdalepl/gvfs-mtp
sudo apt-get update
then
sudo apt-get install gvfs
Restart your computer. You might have to turn on USB Debugging on your Android devices.
Next time when you plug it in, there shouldn’t be any annoying error popups. It should appear in Nautilus as a single device with the SD card and internal memory as sub folders, not as two mounted devices.
Data transfer should work, but you might have a problem accessing the device from some applications, in which case you might want to give Go-mtpfs a try. It requires manual mounting/unmounting the device, (which is done in two clicks) but then everything should be as fast and easy as accessing a normal folder.
It works for me. Ubuntu 12.04 (Precise Pangolin), Samsung Galaxy S III and Nexus 7.