The double Klipsch center speaker setup is disastrous. That is likely to be a comb-filtering nightmare. The Klipsch centers are not very good on their own, and two side-by-side is extremely problematic. The towers are mounted way too high. It's possible the ground bounce cancellation you could be getting in mid-bass would be severe. You may also be seated in an angle where the crossover cancellation leaves a big gap in the response.
You are right that the acoustics of that room are not optimal. Unless you can deploy treatments, you will just have to live with that. "Room Correction" equalization such as Audyssey or YPAO will not be able to help you there.
The AVR is fine. The subwoofer and crossover frequency should be OK. The problem is the room and the speaker setup. First things first, get rid of one of those center speakers. Second, get left and right speakers which have a level height with your ears, in other words, get bookshelf speakers or set the towers on the floor where they belong. Those two things should help. Adding a 2nd sub elsewhere in the room may also be a big help. If you are not able to make big changes to the room, however, it's a doomed enterprise. You can make the sound better, but without improving the acoustics, it will never be great.