I had a few device setup issues (power on/off, entering/exiting standby, etc.) when I recently installed the new yamaha rx-v481 avr. Tried for a little while to use the avr's remote for everything, doing the dance with each device's hdmi cec, standby, etc. Finally gave up and purchased a logitech harmony 650 remote and turned off all hdmi cec and other settings and everything is working great. Plus, the wife is happy with the new hardware now, always a plus. Nothing like getting a text early in the morning when she's trying to watch her recorded shows (the tv's on but I can't hear anything) and I'm in another part of the house with my head wrapped around something complex.
Only thing that I can't change in the harmony is remove power-off commands in an activity. We got into the habit of manually turning off the comcrap dvr via front blue-circle button (on the unit itself) when finished watching cable tv but not wanting to power down everything, so tv had blank screen. If someone turns off the dvr before switching to another harmony activity, the dvr turns back on, because the harmony is doing a power-toggle thing at the end of the watch tv activity (and the comcrap box doesn't have a power-off via ir remote command, which is quite stupid, but comcrap...).
Oh well, just have to change habits a bit. Did I mention the wife is happy with the new system?