The Marantz 5008 is a nice AVR but it does not have all the features you are looking for. It does have 7.2 preouts which may come in handy if you decide to add any external amps.
It also has Audyssey MultEQ XT which may help tame the Klipsch speakers if you have issues with them in your room.
The new Onkyo's have their own new proprietaryAccuEQ that replaces Audyssey, it may or may not be better. I suspect it was a cost savings.
Personally I like Denon, I'm still running an old 3805, and looks like the AVR-X3100W fits your needs so...
And as has been mentioned, I'd also look at a different sub.