I think there are opportunities to reduce cost without reducing performance much in there.
First of all, cabling does not need to cost $500. Absolutely steer clear of Audioquest. Use
Bluejeans cables instead.
The Klipsch THX stuff is good, but you can get speakers that are as good without costing as much. The
Monoprice THX certified in-wall speakers look very promising for the money, although those won't be out till September. A design I like is the
KLH Maxwells, those aren't as expensive as the Klipsch THX speaker and should also be very good. For in-ceiling speakers, I would look at Revel's in-ceilings, and I bet
this one would be very good without the cost of the Klipsch THX one. For the side and back surrounds, look at
this in-wall from Revel.
For subwoofers, I like the SVS 2000 series, but for the kind of home theater that you are building, I would want something a bit more powerful. I would be looking at the 3000 series at the very least, or the 15" subs from Hsu, or the 13" from Outlaw Audio. They will be a bit more expensive but you don't want to skimp on the subs for a impressive home theater. The 12"s from SVS would be good, but you would want more than 2. The 15"s from Monoprice and Paradigm Defiance are also beastly but a fair bit more expensive.
The Marantz is a nice AVR, but I think you are paying a premium for a low profile unit. I would look into Yamaha or Denon instead for the same price.