Hi, Greg. Which Marantz are you looking at? You gave the Yamaha model number for both the Marantz and Yamaha.
coli was getting at the fact that Yamaha uses a different auto calibration algorithm compared to the other two. Yamaha uses YPAO, their own system, and both the Denon and Marantz (if you're looking at a modern one) use Audyssey. I've never used YPAO. I think that Audyssey does a good job for listening positions that are clustered and close in proximity, but it can only store one configuration and is therefore not great for those with more than one distinct listening position (like me). I prefer Pioneer's MCACC system, mostly because it can store up to six configurations if you get a unit with the Advanced MCACC system. In terms of audio quality, I think that Audyssey MultEQ and MCACC are very similar (I haven't used the Audyssey version in the X4000).
The Denon AVR-X4000 got a favorable review here on Audioholics, and the Yamaha RX-A series also seems popular with some folks here. You seem to be looking in the $1000+ range, and that will get you a number of features and connections that the lower-priced models won't have. That said, you might find that a lower-priced model has everything that you want. Receivers have become pretty feature-rich in the $500-$600 range. Are there things in particular that you are wanting?