3.2 Channel with upgraded L/R or 5.2 channel?

Looks like you are looking for an excuse to change a top notch system, just because.   You have gone past the excellent equipment and already invested in dubious tweaks.   Buy more music, more movies. Leave your system as it is. 

Those extra channels make a world of difference. Dropping from 5 to 3 would be huge reduction in the home theater experience. Turn off the rear surrounds for a while.

My primary interest is two channel audio, and I am fortunate to have two systems (see my profile). I used to own Olympica.

Either upgrade the left and right channel… I assume you are using those only for two channel audio or leave things as they are.

Long term, if there was a way to separate the systems you would be doubly rewarded. I find that overall the quality level of home theater is different and fine nuance not important since the video is so distracting. You could plan to extract the best components for your two channel and replace with home theater level components.

I spose if you got money to burn you could upgrade your pioneer avr  to something like anthem or arcam (depending on what you get you might need another amp)--it might sound a little bit better than what you got, but most folks wouldn't notice the difference.

Get rid of the Pioneer Elite receiver  and get a dedicated atmos/object based audio processor (no amp sections shall be in the same chassis) like the Marantz AV10 or higher, depending on what your budget permits. It will let you enjoy the atmos music albums from so many artists, i.e, you should be able to get to a multichannel rig that's not just for movies or games.

Agree with everyone else. Keep the 5 channels absolutely! I too run 5 channels like you but mostly listen in 2 channel. But every time the wife and I watch a movie we really appreciate those surrounds!
 

How about this; add 2 more REL subs? I run 4 SVS’. And whether it’s movies or 2 channel those other 2 subs just added so much more to the experience. I’m not familiar with the Elite unit and whether it has 2 sub outs (via RCA), but if not I would agree upgrade the Elite unit to maybe a Krell Foundation 4K and 2 more subs. This is assuming you would use the RCA and not XLR for your subs. I’ve always gone RCA with my subs..