I'm a fan of both the Helix and the Axe-Fx, in fact lucky or daft enough to own both. Ideally i'd like a blend of both units ! like most of us strange people, I'm are never satisfied ;)
Line 6 Rack Pro's 4 Fx Loops
User interface, it really is a no-brainer
Those lovely capacitive footswitches
Cons Not enough Expression Pedal support, I use all 4 on my Axe-Fx and sometimes have them do 2 functions at the same time
Actually more of a faff to dial in a tone that sits in the mix, not sure quite why, I shall keep digging, its probably me ;)
Axe-Fx Pro's 4 Expression pedals, a must if you are a tinkerer like me and a closet Belew and Torn freak
More Amp and Fx tweaks if you go deeper into the editor
Easier to dial in a Core Tone that sits in a mix, for me that is
Cons That damned Fan, 3 fans later and it still bugs the hell out of me
User Interface is arcane at the best of times, especially if you aren't blessed with good eyesight, it needs the Computer hook up tbh
When it all comes down to it, its a personal preference, the pricing and availability of the Helix make it a much more attractive proposition and I'll happily defend either unit as they are both amazing bits of kit and worth every penny.
We could go on for ages about comparisons etc, its the age old Strat v Les Paul debate, they are just tools, albeit very expensive ones, find what works for you and enjoy it :)