Not a huge fan myself, my dad has a OLDER yamaha reciever (pre HDMI) that has worked for like 15 years. I got him a newer Yamaha and within 6 months it blew the front 2 channels in it and had to get repaired. This is a BIG issue as my dad rarely used it and NEVER cranks it so it was not a overdriven or overused issue. No problems after the repair so far, however not a fan.
Also not a huge fan of their room correction programs.
What you need to look at besides price and feature set (HDMI, airplay, ect) is room correction. You will find 4 different types (I am probably squewering the spelling). Audyssey (used by Onkyo, Denon, Marantz), MCAAC (Pioneer proprietary), YPAO (Yamaha proprietary), and Harman Kardons proprietary room correction.
You will find most folks tend to prefer using Audyssey or MCAAC over the other two and of those Audyssey gets more play in the lower price points.
You are seeing lots of Onkyo because folks can get VERY good deals on refurbs through Parts Express on the older better models (any of the NR-X09 series). The newer Onkyo's are massively cut down on the room correction and I would pass on any of their current under 1k models for the older 09 series in a heartbeat.
So I dont hate Yamaha, but I havent had a good experience with their newer lines and personally prefer either Audyssey or MCAAC for room correction which steer me away from Yamaha entirely.
But pricepoint sometimes is the determining factor. I simply would suggest you compare what you are looking at Yamaha wise to a Onkyo NR-709 or NR-809 as those are my two favorite picks to get in the current refurb line.