Thanks, Thomas, for brainstorming this with me. Yeah, what you said, that's my thinking, pretty much. I hope I'm not biting off more than I can chew in complexity, but here is some more of how I imagine this.
I am familiar with all the Geofex stuff--I have been a member of DIYStompboxes back to the old Ampage days--but I don't think the ability to change the order of pedals globally is worth the added complexity. The only order change I have ever found terribly useful is phasing before or after distortion, but there may be other ways to skin that cat (such as to leave post-distortion phasing to the MS-70-CDR and just stick a small phaser pedal in the same loop as the distortion for pre-distortion phasing), and it's not a deal breaker in any event.
I agree about having independent control of the pedals even after a preset has been selected, and this can take the form of category buttons, as you suggest, or just separate buttons for each switched loop that can be turned on or off regardless of the active preset (with one preset being the null preset, so to speak--everything off until it is turned on). Just that those in a group--distortion/overdrive/preamps, e.g.--would work in a 1-of-n fashion, so that if I select the Fender-style preamp, for example, the Vox-style preamp, the fuzz, the clean preamp and the acoustic simulator are automatically turned off, since I'd never use two of those together. Come to think of it, that may be the only such grouping.
As for compression, I ought to be able to rig a DIY compressor with 2-3 Digipots and a Midi input to control them. This might make more sense than multiple compressors to work with, say, an ethereal ambient-type patch, country-clean, funky rhythm, janglebox, or a singy-sustainy lead patch, going between extremes of super-squishy to always-on-barely-know-it's-there settings.
I also like Tim's idea of having the loop buttons arranged in keyboard format, with a "bank" type switch to convert them on the fly to a bass pedalboard, and maybe an octave and/or tonic switch as well. Tapping out a few notes with my foot every now and then might be fun. I would think it would be possible to program a single momentary switch to select between effect, programming and bass pedal modes, with three LEDs as a mode indicator.
As for display, it is trivial, I think, to have a single LED active with each loop situated right next to each loop switch, but some of the pedal board projects I've seen also implement a small LCD display. I don't know how much more complex this makes things, but I think it would make programming the patches and keeping track of them a lot easier than always having to refer to a cheat sheet.
As for amp channel switching--all my amps are vintage-as-hell. So channel switching probably just means switching inputs, at least for the time being. I think a useful feature here might be separate volume setting at the output buffer optimized for each amp channel, whether set by midi or just a relay/mosfet switch between a pair of pots or buffers, so that signal and noise levels through the pedalboard are kept more or less even, even if the levels going into each amp channel are not. Come to think of it, this is a setting that the "Boost" switch ought to have access to as well.
I know about the USB-2-midi challenge with the MS-70-CDR, but also about Lawrence's work on that, so it seems a solution exists. I assume (but don't know) that the simplest way to go is to program each patch in the MS-70 itself, so that the pedalboard only has to send a single midi code to the MS-70 to select the patch, and not to diddle individual parameters. At the same time, if it is possible, I'd like to be able to activate an external tap tempo and an expression pedal to control certain parameters in certain patches, but I suspect that that is something that will depend on the MS-70, which I don't yet have. Currently, I have an old DOD FX-17 vol-wah pedal on my board, and it has a 5-volt CV output in addition to the standard jacks, so that might be useful. Still, if the board has the option midi control, there has to be a way to program parameters. This may be as simple as a single button to select among available parameters, and a single pot to dial them in. I imagine this gets complicated at the display.
Just FYI, other pedals on board would include an overdrive/boost (probably an SD-1 or Timmy) for stacking with the main gain elements, an octave down, an autofilter, and an echo or delay. I'm assuming that the MS-70 will cover 99% of modulation/delay needs, and kick my vibe, trem, Electric Mistress and one delay off the board, but of course that will be seen. In any case, I think 12 loops (including one to bypass the MS-70) would be plenty, and 15-30 presets in 2-4 banks. Tuning could either be handled by the MS-70, if that turns out to be workable, or by a separate tuner pedal. If it is separate, it need not be part of the system--it would just need a couple of normalled jacks somewhere to patch it in. Same thing for a looper; it doesn't need to be switchable by the system, just patched in just ahead of the output buffer.
Whadya think?