OK, so I've had some time with the Zoom B6 and the Line 6 HX Stomp (and a few years with my Boss MS-3). I've got some initial thoughts, and I've settled on which is going to be on my gigging board, and which will be relegated to home practicing... but first some observations
for those that were interested...
These are just
my opinions and/or observations (some may be unpopular), they are by no means clinical or professional (or even accurate?

), the standard disclaimers apply YMMV, IMHO etc...
Boss Strengths:
-Control Out option for amp channel switching (REALLY like this ability)
-3 FX loops makes it easy to build a board around, the most loops of the group, and in my case they're needed.
-CURNUM function is incredible, if you know, you know.
-Typical durable Boss pedal chassis
-Midi Out (more on this later)
Boss Weaknesses:
-Terrible Display (Tiny, but usable), it's only one of the 3 without color display.
-No parallel routing...Not a deal breaker for me, but I see the advantages.
-Clunky dated PC software...But simple & usable
-Can't bypass the unit, you have to build an FX free patch...Giant PITA, but I've learned to work around it.

-No amp/cab sims, Can't load any IR's
-Luke warm modulation (some great, some meh), subpar drive/dist tones.
-No midi in (not an issue...unless you need it, I didn't)
-Not a fan of the tuner, it's accurate, just not my thing.
-Can't move the loop blocks independently, (you can on the ES-5 & ES-8), I'm surprised Boss didn't offer this on the MS-3.
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HX Stomp Strengths:
-The Helix family has the most robust FX options of the 3, but obviously not all are for bass, but many of them sound just fine on bass.
-PC software was good, it allowed for deep diving, and it was reasonably easy to use...for me, I'm not the most tech savvy...I did find that this software certainly could cause options paralysis LOL.
-Smallest footprint of the 3, not an issue for me, but if you've got a packed board, this may be your ticket to a multi FX.
-Solid pedal build, on par with the Boss offerings.
-Can load your own IR's (I didn't try this)
-Midi in & out.
-Line 6 seems to be pretty good about updates?
-Parallel routing, the only one here that can.
HX Stomp Weaknesses:
-Not a fan of the plugs/jacks on the side, but with a pedal this small it is what it is.
-Not a fan of tuner here either, seems the least accurate of the 3. YMMV
-I'm not a fan of editing FX on the pedal itself...It's much better on the PC IMHO.
-Only 3 switches (but expandable)...This kinda killed it for me, I don't want another pedal, just so I can have more buttons on
this pedal...
-If I use the EXP 1/2 jack to expand the footswitches...then I can't use an expression pedal, maybe there's a work around, but I didn't find it.
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Zoom B6 Strengths:
-Far and away the easiest to edit/build patches
on the unit.
-Though simple, the Zoom had my favorite PC editor.
-Can add your own IR's (I haven't done this yet)
-Records directly into the DAW, comes bundled with Cubase LE, Though recording the standard way through my Presonus interface into Studio One is just fine too, I heard no difference in quality either way.
-Some may say it's gimmicky, but I like the drum machine feature.
-Great looper that's expandable with an SD card (adds more record time).
-Easiest of the 3 to bypass everything...literally push a button, no "programming" needed.
-The only unit here with a touchscreen, but it isn't perfect, it's sometimes a little sluggish.
-The only unit here with a XLR out...Yes, I'm aware the HXS has a "balanced out".
-The 4 DI Sims sounds great.
-The only unit here with dual inputs (if that's a thing you need).
-The tuner here was the best of the 3 hands down, fast & accurate.
Zoom B6 Weaknesses:
-It's friggen
HUGE!!!!
-The only unit here without any Midi capability, pretty egregious oversight IMHO...Really Zoom? I mean the Boss has it (and a fair bit more) for less $$.
-No parallel routing option.
-Though it has 6 available slots for FX in each patch, they can use up the available DSP pretty quickly I'm told, it could make it kinda tough to design complex patches, especially if you use an amp/cab sim...100% transparency, I have yet to build a patch that maxes the available DSP.

-Plastic housing, I find it quite durable, but others may be put off by it...Haven't gigged it, so long term durability is TBD.
-Zoom isn't really well known for supporting their bass products with updates etc...Maybe this will change?
-Kind of clunky to navigate banks/patches on the unit itself, something I can live with if I plan accordingly.
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I ultimately chose (continued using) the MS-3 for my main gigging board, and the B6 for my backup board/practice rig.
I chose the MS-3 for gigging almost exclusively because of the midi option (I needed to be able to control my Aftershock & C4), but I also REALLY like the control out...I use it for amp channel switching, using the CURNUM feature I can literally add my amps drive to any patch I want...I actually preferred the modulation in either of the other 2 units, but I use so little modulation (basically just chorus, a Slow Gear patch and 1 autowah patch) it didn't really factor into my needs list....though at first I thought it would.
The B6 is
almost perfect, the built in DI options & XLR out make it a snap to send a signal to FOH, I added an outboard compressor, to free up one spot so I could do more with building each patch...when you're only working with 6 available slots (DSP dependent), not having to use one of the onboard comps can be handy.
TBH there really isn't a bad choice here, all 3 of these units really are great in their own ways, and what suited my needs/wants may be totally unnecessary for you...