I have my Onkyo TX-NR6100 all setup and calibrated.
To get the 2 main issues brought up, yes the receiver routes the DD signals to the wrong speakers just as my previous TX-NR6050 did. With a 7.1 speaker setup, using a 5.1 DD/DD+ signal, the side surround channels get routed to the wrong back surround speakers just like the TX-NR6050 did. I usually use 7.1 Dolby Surround processing so this shouldn't affect me most of the time except when I listen to Music Concert DD5.1 DVDs.
As far as the Subwoofer output, this is normal and sounds good! The TX-NR6050 must just have inferior electronics or subwoofer processing. The subwoofer out in the 6100 sounds strong and clean. However the 6100 subwoofer output must have a higher output voltage than my 2 Denon receivers. Both Denon receivers had the left/right level at 0 db and the subwoofer at -4db. The Onkyo has the left/right level at 0 db and the subwoofer level at -11 db. The actual subwoofer volume control on the subwoofer has never changed from the Denon to the Onkyo.
The Onkyo does have a lot of advantages over the Denon AVR-S960H. The net radio and apps are excellent to the Denon's poor offerings. Denon has to use HEOS which just sucks. It's very limited in using Tidal and the such and you really need to use the TV display. The Onkyo TX-NR6100 is awesome. I have full functionality of Tidal just as I do on my Chromecast and Android app. Plus with the TX-NR6100, I don't need the TV, I can see everything large and clearly on the Onkyo's front display.
Also with Onkyo, I can setup another pair of speakers on the separate dedicated speaker Zone 2 output connections while still having my full 7.1 speakers connected on their dedicated speaker connections.
Now that this receiver has excellent audio quality for music, unlike the TX-NR6050 I had earlier and returned, I may keep this as my main receiver over the Denon when it comes back.
Plus this receiver has has 3 8K/60p uncompressed HDMI inputs opposed to the Denon's 1 input.
I'm really impressed with the music apps that built right into the Onkyo without having to use a 3rd party app like Heos, Apple, Chromecast, or any other app. Now with the Onkyo you still can, but the music apps are also built directly into the receiver.
The built in native music apps makes me want this over the Denon just for this one, but big, feature.
Also HDMI control works good with my Hisense TV where the Denon's HDMI control worked poorly with the Hisense TV where I needed to turn it off.