The MATE desktop crew released their new 1.6.0 upgrade a few days ago. I've been running it on Ubuntu 12.04.02 LTS. So far, I'm pretty impressed: Smooth, fast, and reliable. A definite improvement over the 1.4 release.
However, the update from 1.4 to 1.6 is causing real problems for many people. Apparently, the 1.4 -> 1.6 migration wasn't actually tested before the release of 1.6. In addition, it seems some 1.4 users may have been upgraded to 1.6 when they thought they were only doing routine updates to 1.4.
So, yes, the 1.4 -> 1.6 migration should have been thoroughly tested. And, no, users ought not to be able to trigger major version upgrades without their express, and obvious, consent.
That said, jumping quickly and blindly into updating any large and complex software system is something to be avoided.
Even with the best intentions and the most thorough testing, no one has any idea what's really running on all the user machines that will be upgraded. Developers cannot know what's been installed on your machine that might blow the upgrade. This is especially true with open source systems like Linux.
Here are three strategies for coping with big upgrades like MATE 1.6.0:
Wait. The Dot One version, of whatever it is, will be along presently, with bug fixes and tweaks. Plus, you will be able to benefit from the experiences of other people who updated early, had problems, and found fixes.
Don't upgrade in place. Instead, do a clean install.
Maintain a separate /home partition and stash configurations files you've edited/created somewhere safe.
My /home partition is on a separate partition (on a separate drive, as well). When I edit or create a config file that resides outside /home, I stash a copy on Dropbox.
So, to update to 1.6, I did a new install of Ubuntu, chose manual partitioning, mounted but did not format /home, installed MATE 1.6, installed Dropbox, copied a few files to the right places, and was good to go.
I've used this approach for a long time on many distributions. While I do upgrade to point releases (e.g., 9.2 to 9.3) in place, I just avoid in-place major point upgrades of complex software like MATE. There are invariably problems, and the best problems are the ones I don't make for myself.