Here are some tips and tricks for those who're still struggling against Fatalis. Some of those tips have already been mentioned by other players, but since such comments are scattered all across this page, I figured it'd be helpful to create a completely new post.
1. Start the battle with a Ghilli Mantle, Heavy Artillery Jewels (ideally inside said Ghillie Mantle) as well as bombs. Equip the mantle, place the bombs in front of Fatalis and then run up to the cannons, picking up some stones along the way. Make sure to hit Fatalis with all ten cannon balls. He will run towards you, triggering your bombs in the process.
2. Use your stones to bring Fatalis down to all fours by flinch-shotting his head. After that, pick up some additional ammo (either more stones or some dragon pods from softening) and wall-bang him. This will combine the damage of the first flinch shot with the damage of the wall-bang and it will enrage him quickly, triggering your Agitator.
3. Tenderize his head if you haven't already. Run up to the ballista and aim some shots at his head and/or chest. If you hit all cannon balls before, this should be enough to exceed the threshold and bring him down. Use this time to inflict significant damage to the head.
4. When healing, try to stay somewhat close to Fatalis. Do not allow him to interrupt your heal (or worse, to kill you) with a fire breath because you are too far away while also making sure that he cannot easily hit you with a tail slam/swipe or charge.
5. You can avoid most fire breath attacks by grappling to his head. Fireballs, on the other hand, will damage you.
6. More often than not, it will appear as if Fatalis is falling down. This, however, is an attack that will damage you and pin you down. Getting hit by that will usually get you killed without outside support.
7. Save your one-shot binders for phase 3 as he is the most dangerous in this phase. This is especially true if you did not manage to break his head at least once. Additionally, always completely empty the Minigun as it will not recharge otherwise.
8. In Phase 3, Fatalis will have a move where he starts breathing fire on one side of his body before performing a full 360 degree spin. Standing behind the front leg on the other side of his body will save you from this attack; otherwise, you can always grapple.
9. The stationary stones in this fight are a blessing and a curse. You can stand behind them to avoid this cone fire breath attacks, but be careful when fighting in front of them, as they will intercept fireballs and bring you into the explosion range. The latter also applies to walls.