I've been in a similar situation when the QC released. I had the FM3, Helix Floor and QC at the same time and extensively compared them back to back.
I ended up keeping the FM3, because I felt it was a mature product, it was more desktop friendly size than the Helix, and best sounding overall. The Axe-Fx 3 is all that too, which is why I bought one used at a reasonable price around FM9 release in the US (several months before its EU release).
In hindsight, I wish I had kept the FM3. Like you, I ended up not using all the capabilities of the Axe-Fx 3. With the gapless switching etc I think it would be more than enough for my needs, apart from the onboard UI.
I like the Helix except for its size. For me crouching down to adjust stuff on the floor regularly is just uncomfortable due to some health issues, and it's too big to use on a desk or stand IMO. HX Stomp is too gimped on onboard user interface.
I really wanted to love the QC. The form factor was great and I liked the user interface and having lots of knobs. At the time I was just unsure about its firmware update cadence, and it turns out I was right as it took them a long time to get the editor out etc. The effects quality was my biggest beef about the unit. It's "fine
" but not awesome.
You can probably see where my progression to liking the Hotone Ampero 2 Stomp comes from. It's basically a cheap QC in HX Stomp form factor now that it can also create captures. Of course, I'm not saying you should buy one because you are unlikely to be happy with its fx quality compared to what you have. I'm just not spending Helix/QC/Fractal money again for current gen products.
Axe FX III - Super capable device, but I use about 20% of its capabilities, about 30% of the time. The rack format is starting to annoy me too, because most of the time when I do use it, I'm using it in tandem with a valve amp.
So here your main issue is form factor and not making good use of it, which are relatively small problems compared to what you list for the others. That puts the Axe-Fx 3 still at the top of your list.
Helix - I'm really familiar with it, and have been a fangurl since 2016. I've plunged the depth of it though, and I'm no longer happy with the reverbs and most of the delays, and ultimately I'm just kinda bored with it.
Being bored with something is not a good reason to swap it, might mean it's just doing its job for you. But not liking the delays and reverbs is a valid reason to get rid of it.
Quad Cortex - it is the newest device, and I really like the sound of the amps. The effects are basic. It doesn't work in a bigger rig setup or 4-cable-method very well, and it really is just kind of a desktop only device, or a posers device (I'm half joking there!) and ultimately.. I really don't see it as a good long term investment.
Sounds like the QC is already close to being out when you list more drawbacks than with the others.
It is 2025. I'm intending on pairing down some gear, paying off some debt, and in general trying to settle down on some trusted and gear I can sit with for the long-term (say, the next 4 years) - I will of course have some dalliances, but some upcoming life changes will mean I won't have much disposable cash for a couple of years, and I will need to really focus on music rather than gear anyway.
But since we chat so much shit here anyway, I thought.. what's one more thread going to hurt?!
I'm leaning to Axe FX III.... or selling the Helix and Quad Cortex, and getting the FM9, and just going all in on Fractal. Keep the AxeIII for studio, FM9 for giggage, sell the FC12, and pay off a bit of credit card from that.
With Fractal pricing being pretty hideous in Europe and used FM9s seem to be very hard to get... Maybe you can sell the FC12 and keep two units: Axe-Fx 3 for the studio, and either Helix or QC for gigs? Then it just comes down to whether Helix's better footswitching is worth its big size over the QC's more portable form factor. Or maybe you can use your pedals for gigs instead.
I think it's much easier to compromise on fx quality for gig uses where "solid but unremarkable" is alright when you have multiple instruments blaring around you at loud volume.