One solution is to install both Ubuntu versions on your computer either on different disks if you have multiple or on different partitions of one disk and dual-boot between them.
To avoid the duplication of configurations you speak of, you can **use the same home directory** on both installs.
As your home directory contains all your user specific configuration there is very little duplication I can think of.
(Exceptions I think are Wifi connections if they are configured to be used by all users and printers.)
**I've used this successfully with Ubuntu 12.04 , 14.04 and 16.04.**
There could be issues if some software uses the same configurations files differently on different Ubuntu versions.
But I had no problems like that so far with any software I use.
I don't use the Unity desktop, so I don't know if this might give your problems, when switching back and forth between different versions.
My gnome fallback/flashback session had no problem with that.
**Nevertheless I'd recommend backing up at least your home directory, better also your root partition, especially if you need to resize your partitions!**
How to share the same home directory depends a bit on your partition setup.
The default in Ubuntu is to have the home directory on the same partition as the root system.
If this the case for you and you have Ubuntu 14.04 already installed, install Ubuntu 16.04 in a new root partition beside it (resize current partitions to make space if needed).
Then boot into your new Ubuntu 16.04 installation and mount the 14.04 root into e.g. /mnt/root_14.04 by editing /etc/fstab or using the graphical tool Disks.
You can then either change your user's home directory in /etc/passwd to point to /mnt/root_14.04/home/USERNAME or mount bind /mnt/root_14.04/home to /home in fstab.
After a reboot you then use the same home directory in both systems.
You will need to adjust your ~/.bashrc file to source the right ROS setup.bash depending on which Ubuntu version is running.
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