I have the same sort of issues Bill,
I spent quite a long time, (too long!), yesterday comparing tones by plugging my guitar directly into my Focusrite soundcard using a plethora of plugins but nothing sounded as good as via the M13. It just sounds beefier and fuller, (and yep, I did set the impedance correctly).
I've settled on using my computer in an effects loop from the M13 now. This gives me the best of both tonal worlds and if it all goes tits up, so to speak, I can still change to an M13 patch without an effects loop in line since the effects loop settings are patch specific.
It also allows me to set up some cool loops between different pieces of music live which won't mute when I'm changing patches on the computer.
> From: firstname.lastname@example.org
> To: Loopers-Delight@loopers-delight.com
> Subject: Sound vs function
> Date: Thu, 16 Jun 2011 19:55:07 -0700
> As a fellow tone snob I feel your pain, I'm still stuck in hardware
> mode and I'm able to do what you want with out involving a computer,
> but there are few hardware choices available that can do multiple
> loops and mine, the LP-1 is currently out of production and the
> roland rc 50 has been discontinued. When the time comes for me to move
> to software I will still continue to use a small hardware front end
> and smaller floor looper as both a safety net and also because I
> still prefer analog, even solid state over modeling for guitar tones.
> To wit, my Custom Tones Ethos preamp offers a scant two channels of
> guitar tone, essentially a clean and a dirty channel with an extra
> boost on the dirty channel, but it has an excellent speaker emulator
> output, so I can get great guitar tones even if I have to run direct.
> Its like a dumble amp in a box, and I'm fortunate enough to have
> played a few in my time. Effects are another matter as i can really
> see putting a lap top to good use with both pre and post effects.
> Right now I tend to have my effects pre loop when playing live and
> honestly I like the fact that my ethos and M-9 and timefactor and
> other effects are easy to change on the fly, the frustration I have
> found with all in one modeling/effects amps is how clumsy they have
> tended to be when needing to change eq and parameter settings on the
> fly. To much bass for the room? what are you going to do, tweak every
> preset you have created each time you move to a new one? i think the
> new modeling amp choices are much better than when I was using them ,
> and they have addressed a number of these issues, but they still feel
> and sound a bit flat to my ears. Plus I'm a bit tired of endless
> menus, and LCD screens. Time spent editing effects parameters and
> learning new platforms is time not making music, and currently I'm
> more interested in making music with the tools I have, which as of yet
> have not proved limiting. So if I was making the leap, I think i'd
> keep as much analog front end as possible, but keep it simple, and use
> a combo of Abelton and Mobius, becaues cool people in the know said
> so, and because Jeff Larson has a dog almost as cute as mine , and
> what ever cool plugs I could get my hands on, I would start to
> integrate...slowly. I'd start with some Expert Sleepers stuff,
> because Os makes cool plugins, and I'd become an absolute pest to
> many of you on this list.