The balancing in the game isn't done really yet. Its all placeholder stuff.

The 2 handers scale technically a bit better and can deal with crowds better. You have to remember that a lot of stuff in this game scales off your skill with that weapon. And the higher the damage multipliers, the better they do later on.

Also the 2 handed axe has no multi-target penalty. So if you hit multiple targets, they all get the juicy dmg. Where as you will do less damage with the 1 handed axe when hitting multiple things.

I still like to use the 2 handed axe when I get it to deal with hordes of things. It definitely could use some buffing or changes in the swing times/animations, but its not terrible.