The third desktop option for Linux Mint users is known as Cinnamon. While it must be installed manually from your package manager, it's by far the best of the available desktop environments for Linux Mint. Also using the Gnome Shell, Cinnamon offers users a level of control ranging from the desktop applets to overall desktop effects.
Despite the newness of this desktop environment, Cinnamon has proven to be a fan-favorite not only on Linux Mint, but with other distributions as well. Best of all, it's laid out in such a way that anyone coming from Gnome 2 will feel right at home.
One area that frustrates me with Ubuntu is that they don't clearly mark how dangerous some package updates can be. This isn't to say that some updates that could create problems aren't important, rather that Ubuntu needs to provide a better way to customize how software packages are being updated. Because this could potentially eliminate problems new users face.
Linux Mint, on the other hand, uses a level-based numbering system. Level 5 is the most "dangerous" and Level 1 is totally trusted, so you're in complete control as to what's updated and how. Linux Mint also allows its users to choose the update level automatically or manually, so nothing is broken by surprise by an update.
As great as the Linux Mint software update approach is, there's still a problem that may have been overlooked. Because Kernel updates are important, if a kernel update is always labeled at level 5 (dangerous), there's a likelihood it's not going to be installed. On Ubuntu, this is a moot point as updates are all or nothing by default.
So from a security perspective, it's a valid argument that Ubuntu's policy may be more secure. However, I prefer the Linux Mint approach to package management. It keeps me in control, without having to skim through what packages are selected and which ones aren't.
Software backup considerations
Another major difference is how software is handled from a backup perspective. Since neither Linux Mint or Ubuntu offer you a fool-proof, pre-installation method of doing simple dedicated partitions for home directories, data and software backups become quite critical as a result.
Both applications allow you to back up local directories to Dropbox/UbuntuOne based-folders if you wish. Where Ubuntu completely drops the ball, however, is not providing application specific backups. Linux Mint's mintBackup however, does offer this type of backup option.
One area mintBackup lacks in is with the ability to do incremental backups like Déjà Dup. Since incremental backups take less time to do than a complete backup, some users may find that mintBackup isn't the best way to handle directory backups on a regular basis.
So here's my advice on the matter: use mintBackup (Ubuntu PPA here) to handle your software needs, while relying on Déjà Dup for a good incremental option. Remember, the wonderful thing about these two distributions is that you can use the same software on both installations.
Upgrading to a new release
The final area where Linux Mint and Ubuntu differ is how users are supposed to upgrade. Since neither of these two operating systems are "rolling release"-based distributions (excluding LMDE, most users are tempted to simply install upgrades in place instead of doing a clean installation. Ubuntu goes so far as to offer a distribution upgrade option.