I just picked up my Nexus 6 finally and I did several restarts to get the backup i wanted. But from downloading my apps and getting activated does that make it really warm? I can feel it through my Spigen case.
I think pretty much every phone when I've taken it out of the box and started installing all of my apps and what not in one big session... they always got warm. When I was done with everything, things were fine, though... Unless I played a game for a long time... (Most notably when I had an Xperia Z2...)