I'm in a very similar position. I have the Onkyo TX-NR1007. It's been great. I have no problems with it and I hope I won't have any problems since I purchased new and have always had the AVR on top of my AV shelf with the top exposed to open air - thus no heat build up. I know that doesn't exempt me from potential issues but it should help! As to the HDMI problems you are worried about on yours, from what I've read Onkyo usually will give a 1 time out of warranty assistance from what I've read - have you contacted them to see if they would help you?
As to my next unit, I've been doing a bit of research and am primarily interested in another Onkyo, an Integra, a Denon, Marantz, or perhaps a Yamaha. I want to stay mainstream to avoid buggy botique brand issues. I would prefer XLR outputs, because I have a little tiny bit of hum from my AVR to Sherbourn 7-350 amp and Crown XLS-5000 amp that I can't seem to ditch and I'm hoping true XLR connections out would fix that. I use the Audyssey on my current 1007 only to setup distances and levels - then turn it off. I purchased a TX-NR818, but thought it was a bit of a downgrade from my TX-NR1007 in feature set, despite being XT32 and so sold it a couple weeks later.
Since I don't usually keep Audyssey on, then I'm not tied to Denon or Onkyo or Marantz or Integra. Another thing I've found very valuable is having independant subwoofer controls from the AVR. It wouldn't be a deal breaker to have a single sub out - but it's a big bonus to my interest level if it does. I use one of my sub outs for my buttkickers, and the other for my caps. I can adjust either level on the fly, and set unique distances. If I didn't have two sub outs I couldn't quickly adjust levels on one or the other without getting out of my theater seat and turning the gain dial on the amp. LAME. Three subwoofer outs would even be better - as the Yamaha has (I think). Then I could control the caps, my buttkickers, and the new sealed I'm putting together soon with the remote.
As another bonus I'd like to be able to control the unit through an android device, and our Onkyo TX-NRx007 units are one year before that worked mainstream.
The easier and cleaner the onscreen gui the better. It's also a must to be able to adjust subwoofer levels on the fly, cause I'm constantly tinkering with either my sub levels or the buttkicker levels song to song. The Onkyo 1007 does fine in this regard as I can get there in a few clicks and adjust subwoofer 1 and subwoofer 2 output without pausing or otherwise stopping my media.