It isn't the thickness that is the problem. I've been carrying around a flip phone that is more than twice as thick as the Nexus 5 and it doesn't bother me. But the corners of the Nexus 5 poke into my leg when I'm walking or sitting, and I'm afraid that the pressure being put onto the Nexus 5 when I'm sitting could cause the screen to crack. The only thing that would help is if I started wearing baggy pants, but I'm not changing my clothing for the phone.
I don't blame you there haha. How do you pocket your phone? I put mine upside down the the screen facing my leg and haven't felt a poke yet.