I have both, and although the Axe is £1000 more, I'd say it's infinitely better value for money
As
Dave Merrill said, the capacitive touch knobs on the Helix are very handy and having control over 64 separate parameters per preset is great, though I wouldn't swap that for the Axe's channels system. The UI on the Helix is simpler, but I'd say that's because the device itself is less complicated. It's meters, which were a bolted on afterthought, are laughable.
I can get some decent sounds out of the Helix, but it takes more fiddling and time to do so than with the Axe, and the resulting tones are not nearly as satisfying. We have hundreds more amps and cabs to choose from, with pages and pages of things to twiddle with. The depth and breadth of the Axe's arsenal of effects is astounding and on a completely different level to Line 6's, quality wise.
I'm on the waiting list for the FM3, once I get it I'd like to sell the Helix, but I probably won't because some of it's buttons have become squidgy and unresponsive, every time I move the joystick selector knob it feels like it's going to break.
The Helix editing software, HX Edit, is not very good at all. It uses fiddly thin lines which are difficult to 'grab' hold of with the mouse rather than our nice big clear knobs and switches. I find it very frustrating to use.
The last Helix firmware update was in April, what have we had, 10, 15 updates since then? How is it that a tiny company like FAS, when compared to the monster that is Yamaha, can deliver so much more? Maybe the question should be the other way around.
And finally, there's the Helix forum, which is ruined by a handful of power users, who take any comment which is not a glowing endorsement, as a personal insult.
Pound for pound, the AXE leaves the Helix standing IMO.