Sonus faber choices - help me decide

One more question. Assuming I stay in the Nova line, my decision to go with the Nova II was largely because I have subs that will handle the last octave. I didn't think paying $5000 more for a a ~5Hz difference was worth the money required to step up to the Nova III. Is this logic sound? My assumption is that the only difference between the II and III is bass extension. They have the same cabinet, tweeter, and mid-range driver, after all. The III just has one more woofer.

-Well both will be much better than the B&W CDM 9NT so no worries there but if you have the means always buy the better speaker.  Futuras Is an endgame speaker IMO  

-the first question I have is how do you use your subs? Do you highpass (cut the lows to the mains) if not you should be. This will play a big part is what way to go. The main difference between a lot of speakers is just the bass and if you are cutting it off anyway it matters a lot less.
 
-the soundstage and inner detail will most likely be stripped out a bit by the denon it will just sound like it has less scale. I also have a combination two channel home theater and speak from experience (I have had many systems with denon, marantz, b&w 703s (newer version of your speakers) and I run duel subs (picture of my system in my profile). Anyway the kicker is you probably use your denon for bass management and that will make it hard to go to a two channel pre-amp if you ever want to (you should) because you would not only need to bypass the surround through the two channel pre amp but also through an external crossover. For what is is worth I do just that. Have a two channel preamp/amp with “external” crossovers in the subs and bypass through the two channel system for home theater. Works great, best of both worlds but is a lot of wires and equipment. Also family members will never be able to turn it on again, you can decide if that is good or bad lol. 
 

I cross over the subs in the Denon @ 40Hz. The CDMs go down to ~38, so I thought 40Hz would be a good choice. I have experimented with higher crossovers, but don't have a real preference. At one point I ran Audyssey and told it that I only had two main speakers and was shocked at how great the bass was from the 9NTs (without the subs). I was still missing the deep lows, so I eventually did run it again and tell it I have subs. That is where I am now: 2.2 on Audyssey Preset 1 @40Hz. Preset 2 is for my 7.2.4 setup.

I have my eye on the Anthem STR integrated amp. It has ARC and supports bass management. I figured I would use the HT bypass for the main speakers and then do a bunch of Y splitting for my subs. I assume the Anthem would integrate the subs similar to the way the Denon does, and I would not blow up my subs by having them connected to both amps. I would just turn off the Denon when I'm running two-channel (and vice versa). The good thing about the Futuras is that they go down to 25Hz so I would not even need the subs in that configuration.

Given that, I still wonder if I should shoot for the higher-end speakers. Would the Anthem drive them appropriately (Stereo integrated amplifier with 200W/400W/550W into 8/4/2 ohms)?

I need to make a decision today. The Nova II's are on order and I need to tell the store if I am going to cancel the order. The guy with the Futuras will not have them forever. I'm assuming they will be snatched up soon.

Before buying the Anthem STR integrated amp, you should know that Anthem also makes the STR preamp, which has a more sophisticated ability to independently integrate not only one, but two subs with ARC correction and also use them when you are doing home theater. So, you may not even need the Y splitting for your subs.

You already have a power amp for the front L/R channels, so I'm not sure why you would need the STR Integrated amp at all. 

I'm not sure the STR Integrated will drive your front L/R speakers any better than your 200 wpc Rotel.

As to the speakers, I'm a sucker for big floor standers, so I would be all over the Amati's if I could swing it!

Well I would take the better speaker every time. 
 

yes you can connect most subs to both a two channel preamp and receiver at the same time. It is important to have the inputs sum. If they don’t it will not work so read your manual or give them a call. I do this with my JLs and it works well.
 

I would also encourage a higher crossover. Your subs are better than the speakers below 80hz for sure. Try 60, I bet you get more impact and lose nothing.