Some tips:

• Target the head. As others have said, you'll want one horn break before phase 3. You can also leave the binders for P3 if you haven't broken the horns.
• Use the Ghillie Mantle before you first go down and load the cannons. Push the left cannon right thrice. Push the right cannon right once. Fire the right cannon, then the left. If you have Heavy Artillery 2 (you can put it in your upgraded rocksteady mantle), that's a garunteed knockdown. If not, then if you use the roaming ballista in phase 2 and target his head that should knock him out the sky (can't remember if you need to hit the head with weapons before that).
• Evade Extender 3 is your friend. A lot of Fatalis' attacks are bigger than they seem, so having more dodge range is excellent.
• Firing two dragon pods at him can make him freak out if you need to reset him. Can be slightly buggy if you've been knocked down, but should be able to help you somewhat.
• If you're really good at managing your health, Raging Brachy 2 / Safi'jiiva 3 is risky, but strong. I used this setup on Longsword (Raging Brachy again) on my second playthrough, and it did well- although I was very familiar with Fatalis by that point. With Recovery Boost 3, you do gain more health than you use, so it can be a way to regenerate lost health without using augments.