When the Nexus 6 review was published, I commented that there were performance issues that weren't present on the Nexus 5 running Android Lollipop. Many users commented that the FDE may have been to blame. Like I mentioned earlier, Motorola provided us with a build of Android with FDE disabled.
Unfortunately, I haven't noticed any improvements to many of the areas where there are significant frame rate issues such as Messenger and Calendar. I speculated in the Nexus 6 review that the performance issues may simply be the result of insufficient GPU performance or memory bandwidth to drive the QHD display.