just wanted to chime in on this- I bought a used M13 two days ago; I also use the JTV59 and HD500. *Loving* the M13. This thing is amazing!
I am running it in the effects loop of the HD500 as my "post" effects processor. I am using a TRS splitter to run the HD500 fx loop in stereo to and from the M13.
The one thing I didn't fully comprehend and/or appreciate about the design of the M13, is the amount of "on deck" effects - as you mentioned, basically twelve stomp boxes each with on/off footswitch - and all able to be configured / saved in presets. Four "on" at any given time.
And the manner in which the footswitches work is nice - it just switches between the effects defined in each "fx" stack (across, 1-4, down, A,B,C.)
It's been great for doing some crazy cool combinations of mods, delays and reverbs. And I am running dual amp paths, panning them hard left/right in the mixer before it hits the M13 - the ping pong and stereo effects sound pretty stellar routed through the HD500 effects loop. Something about that configuration just worked really well.
I was also able to integrate my "pre amp model" analog pedalboard into the rig, and everything sounded stellar together. It got late (two nights in a row! lots of coffee making work do-able today) so I switched out of using the DT25, and just ran the 1/4" outs from the HD500 into my soundcard and monitored through some M-Audio speakers. The stereo effects are really nice when you have the speakers spread wide and you sit in the sweet spot.
I can see how stereo is complex though, and presents unique challenges when creating a live sound, vs home studio noodling! Even just panning the two amp models center vs wide left/right made a fair bit of difference in the tone; and the stereo ping-pong sounds good regardless of the source feeding it, mono or stereo.