Haven't done Helium, but one of the big differences is that you retain all rights to your work (you don't share it). So you could turn around and sell the same piece elsewhere (including AC).
Helium doesn't offer upfront payment, AC may pay upfront in addition to the rate of $1.50/1000 views, but not necessarily. From what I was told by others who write at Helium, they earn more at Helium in the long run.
Helium also has a funky rating system. It considers all the pieces on the same topic, readers then rate those articles. The best of the articles in that topic will rank higher when searched. Most writers that I spoke too aren't too thrilled with that feature because it doesn't necessarily reflect how well written a piece is- but on popularity.