Thanks for the input. I've been playing around more and even been able to make auto-pause work. In my opinion, Parallels 11 is WAY too sensitive about what's considered an open/running app. I've basically had to disable a lot of services that didn't previously register as activity to stop pausing.
The GoToMeeting app allows for quick launching of a meeting. It's not a full app, does need to be launched, and doesn't appear as a running app. However, it prevents Parallels from pausing. Also, I use NetExtender for VPN access. When a connection is active, Parallels 11 will not pause (10 had no issue here). I used to like having the VPN connection there to always come back when needed, but now I have to either manually pause or disconnect for auto-pause to occur. These kinds of things shouldn't be considered "open apps" and should allow pausing.