I also have most HDMI features disabled with the exception of ARC. The communication between HDMI ports gets random and uncontrollable. Especially frustrating is when I would try and switch between cable box, HTPC, BD player etc. with the AVR and it would keep defaulting to one unit. Sometimes it would be the BD player, other times it might be the cable box.
I have been pleased when using apps on my phone to control cable boxes, TVs and the AVR over the wifi network.