I only ever fought fatalis maybe a little over half a dozen times in my freedom and unite days. Everytime the group failed except once. I just hate the thought of losing long battles at the 30th minute mark through no fault of my own. That is what scares me. That and half a life bar draining attacks.
Well, fatalis was one of the few monsters in the game where damage done to his health would carry over from your last battle with it. It led to a fun exploit where someone with a nearly dead fatalis would repeatedly start the quest and restart his PSP right before the end of the quest so that the rest of the team could farm fata parts.
Some parts could only be farmed from a completely healthy fata, though.
I'm not sure why Capcom decided not to have anything like those multi-episodic quests in Tri. Elder dragons also exhibited a little bit of this as well. If you did enough damage, they would flee and the quest would be considered an overall success without an opportunity to carve from anything other than the tail. The next time you fought that particular elder dragon, its health would be completely restored, but it would be missing a tail (if you had cut off the tail earlier).
Neat touches like that are the reason I still think more fondly of Freedom 2 and Unite than I do of Tri or Third.