Both signal routing within the patch and hardware I/O, actually. Let me try to explain without letting it spiral into too much detail. 
The main issue I had with the Helix was that I always want to run delay and reverb in parallel. To me, that gives a much clearer tone—compared to delay feeding into reverb, where each delay repeat ends up with its own reverb tail (which I don’t want). I also wanted to split the signal so one output would go to FoH with an IR applied, and another would go to my real tube head and cab—so without an IR.
Signal routing on the Helix is a bit limited. You essentially get two processors, each of which can be split once into an A and B path. The delay and reverb blocks I wanted to run in parallel were late in the signal chain, so they had to live on processor 2. That meant I had to use the split there, which left me no way to also split at the very end for IR vs non-IR outputs. To work around that, I added a send block at the end, which fed into an external IR loader (Two Notes CABM+). It worked, but it meant more gear, more wiring, and a setup that was harder to tweak.
On top of that, when using in-ears, you often want some extra effects only in your monitors—not going to FoH or any cabs. That wasn’t possible with the Helix at all, so I had to use a small mixer and an external reverb pedal just for that. It all got a bit too complicated.
Here’s a picture of the Helix-based board with my main patch loaded. If you zoom in, you’ll see how processor 2 is split to run delay in parallel with reverb. And because of the extra hardware, I had to mount the already heavy Helix on a pedalboard—so yeah, it was a bit bulky. But it did sound great!
With the Fractal gear, you get complete freedom in signal routing—you can split and merge signals as much as you like within a grid layout. One of the really cool things is that I can receive the band’s monitor mix as “Input 3,” and then blend in as much of my own guitar signal as I want. I can even apply EQ and effects separately to both the band mix and my own signal, just for my in-ears.
In my current setup, “Out1” goes to my on-stage cabs, “Out2” is sent to FoH, and “Out3” is my personal in-ear mix.
This is what I use now when I need to stay really compact and low-volume (though if space and volume allow, I’ll sometimes bring two of the small FRFR cabs).