Steps to reproduce the issue

I have had the same thing occur with three different sites. All were 2.5.14 up to 2.5.28. I updated them all to 2.5.28 using the Joomla updater. Uninstalled everything that wasn't core Joomla just to be safe, and then ran the 3.6 update via the updater.

Expected result

Successful upgrade to 3.6

Actual result

In each case I received the same error as detailed in the forum post: http://forum.joomla.org/viewtopic.php?f=710&t=929251

System information (as much as possible)

Setting Value

PHP Built On Linux server1.silverdolphinsolutions.com 2.6.32-642.1.1.el6.x86_64 #1 SMP Tue May 31 21:57:07 UTC 2016 x86_64
Database Version 5.6.30
Database Collation latin1_swedish_ci
Database Connection Collation utf8mb4_general_ci
PHP Version 5.6.23
Web Server Apache/2.4.18 (Unix) OpenSSL/1.0.1e-fips mod_bwlimited/1.4
WebServer to PHP Interface cgi-fcgi
Joomla! Version Joomla! 3.6.0 Stable [ Noether ] 12-July-2016 21:14 GMT
Joomla! Platform Version Joomla Platform 13.1.0 Stable [ Curiosity ] 24-Apr-2013 00:00 GMT
User Agent Mozilla/5.0 (Windows NT 10.0; WOW64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/51.0.2704.103 Safari/537.36

Additional comments

I was eventually able to get the site mostly fixed and runing on 3.6 by following the steps shown in this forum post: http://forum.joomla.org/viewtopic.php?f=710&t=928848 however after following those steps I still have a back end control panel that only loads the text and not the template. However if I click through any of those links the other back end pages load correctly.