Well if you are comparing them with the same subwoofer, it is less likely, but if you have $600 extra, and put some of that towards a better sub, you will increase the performance of the Pioneer system. A better sub will be more articulate and dig deeper, and not sound as boomy. I would establish a budget and then compare the setups at that budget. So if you have say $1000, then you can get a great sub to go with the Pioneers, versus a weaker sub with the Klipsch.
I would go for something like the SVS-PB1000 to pair with the Pioneers. You don't need to play it loud, but it will offer good bass and blend better with your speakers.
Samsung PN60F5300 | Denon DBP-1611 | Roku 3
Denon AVR-1713 | EMP E55Ti | EMP E56Ci | EMP E5Bi | BIC F-12
Topping TP23 | NHT SuperZero 2.0 | Velodyne DEQ-8R