For me, the biggest upgrade with the Helix modeling was the fact that they incoporated IR's. That was the HUGE downfall with the HD stuff for me and many others. The models were fine. They were an improvement over the XT/X3 generation. It was their cab sim technology that was so outdated for the time, especially when you compared it to the Fractal stuff which incoporated IR's since the very begginning.
I've read the Helix software was built "from the ground up", but I have a hard time believing that. Especially because the Line 6 modelling was never bad. It was just the cabs that really pulled it back. And suspiciously, you also get some HD models in the Helix stuff.
Even when the Helix stuff first started, their stock cabs were pretty bad, LOL. It was only since the latest update that they completely redid them (I think it was November last year?) that they became decent-sounding. And even then, I'd still much rather run some high-quality IR's like OwnHammer or Celestion Plus, personally.
That being said though, the Fractal stuff's modeling is just on another level. Not only do their models are more in depth with what you can tweak, but the quality of the sound is just better. Granted, if you run the same IR in both, the difference in quality is not night-and-day, but once you put them both in a mix under the microscope, you can tell. There is just more depth and detail to the Fractal stuff.
Which is a shame, because the HX Stomp is comparatively cheap, but the the top-of-the-line Helix stuff uses the same modelling algorithms and sound, and is pretty much in the same price range as the Fractal stuff.
JMO.