Low call volume on Nexus 5 Lollipop
Backup your data and reset the phone.

I had the exact same problem, the way I fixed it is by doing a factory reset. To nail down the problem, I booted up the phone into safe mode (Long press the 'Power Off' on your power menu). There, it was better, so I decided to wipe my phone and recover my data afterwards using TWRP. Also, you should note that 5.0.1 sort of improved the speakers - both of them, the earpiece and the actual speaker.