I'm familiar enough with the Yamaha pre-pro. XLR pre-outs are nice if you need them, but all my gear is generally close together so no advantage for me there nor any gear particularly needing xlr/trs connections, rcas work just fine. Might be nice for a mixing board, tho. I use an older bluray player in the one system I use zone 2 in, and it does have analog outs in addition to hdmi to help out when I want to play audio in zone 2 thru it.
Here's info on the old hdmi/network board issue
https://www.avsforum.com/threads/onkyo-acknowledges-failed-units-and-extending-warrranties-until-2018.1652514/
My Onkyo failure experience was different, been a while now but seems it just failed on hdmi inputs altogether. I had an older Pioneer that also had hdmi issues, and eventually went up in a puff of blue smoke while still using some of the functioning analog/digital inputs aside from hdmi. Not sure what you mean about the Onkyo's internal amps, the zone 2 use of internal amps would depend on your setup....would need to know more about how you set things up in the avr.
I love the multich audio, that's why I have four setups using such (avrs in all of them). Grew up using 2ch as there was no choice, like music being mostly vinyl or FM radio

. I have no desire for "stereo" subs, prefer to place my subs where they work best for room smoothing....use four in my main system...still fine stereo sound from L/R speakers even if I use just 2ch modes.....my older 2ch gear is not used much, have one setup in a spare bedroom to use some of it but lacking so many convenient features found in an avr for digital audio and bass management aside from of course not being able to handle multich audio.