kamui can make amaterasu go away, amaterasu can't make kamui go away. Amaterasu while strong has been shown to be much often take time to burn rather than burn instantly (though in some cases it does burn instantly). While kamui is instant or near instant all the time. So kamui has the speed and has the ability to get rid of the other one. Also with both forms of kamui (obito's and kakashi's) the kamui user is essentially invincible. Even if you made an amaterasu clad sussano, you still wouldn't be invincible, especially not to a kamui user.
Edit: OH YES, I also forgot! Amaterasu can be sealed, while kamui can't (as far as we know)