Subwoofer:
IMHO any of the three subs you listed should provide a noticeable improvement over the PDR-12 (only 110W RMS).
However, size of room (cu. ft.) and intended primary use (movies vs. music) are important factors in a sub decision.
- You have a ported sub now, that may indicate the PB-2000 is a more appropriate choice for your room; the other two (SB-2000 and JL Audio) are sealed subs.
- Based on MSRP, you can buy two PB-2000s for the price of one JL Audio E-110.
AVR:
You will probably will not notice an improvement in SQ from a receiver change.
The main reason to change an AVR is to get access to newer codecs (ATMOS, 4k, UHD, etc.), better room correction software, or an improved user interface (BT, WIFI, etc).
- The Denon and Marantz provide an increase in power at 125W/ch (8 ohm, 2 channels) and 110W/ch (8 ohm, 2 channels) respectively vs. the Pioneer's 80W (8 ohm, 2 channels)--but neither increase is large enough to be noticeable (normally it takes about a doubling of power to get much noticeable improvement in SQ).
- The Denon or Marantz both use Audyssey instead of MCACC for room correction; you can find arguments in favor of both systems, although Audyssey is more common. I have not used MCACC, but do prefer Audyssey over YPAO (Yamaha's RC software).
So in short, spend your upgrade money on better/more subs unless there is a codec/RC/user interface issue you need to solve.
Cheers,
XEagleDriver