I just found this post again, and apparently according to Paul Murgatroyd we will be looking into changing the mht format soon. Although I still don't think it will be in SEP 12 since that is not an upgrade from SEP 11. I will try to keep people posted on this as we hear more. Hope this makes everyone a little happier : )
We are looking into changing the format due to both inability to read the files on mobile devices and the fact that newer mail servers tend to block them.
At this moment in time there is no way to change them though, we are also looking at adding more information to the alert emails
Paul Murgatroyd
Principal Regional Product Manager, Enterprise Security Group, Symantec
The full forum where I got this from is here:
https://www-secure.symantec.com/connect/forums/mht-files-not-opening-blackberry-or-iphone