The Yamaha has more inputs and outputs, and also has the option of front "Presence" channels.
I personally would go with the Yamaha, largely because I have had excellent experience with them in the past, and, judging from online complaints that people make about various brands, Yamaha seems to be as reliable as you can get. That said, I don't think that Denon is a bad choice.
The room calibration issue with Yamaha is that they don't automatically equalize the deep bass. They set the levels and delays just fine, but only automatically equalize above about 60 Hz, so that the deep bass below that is what it is in your room, and the Yamaha will not correct the frequency response. Although that is not ideal, it is not much of a problem. Again, it does set the overall level right and the delay right.
I have not heard the speakers, so I have nothing to say about them. But I did look at the specifications and upgrading the subwoofer to an SVS is a good idea.
Basically, you seem to be picking decent gear for the money.