Out of the games that I beat the final bosses for, I would have to go with...
Great Redips - Mega Man X: Command Mission
Shit goes down in this fight. If you use the wrong parties, you are fucked. If you get unlucky, you are fucked. Part 1 of the fight is all about survival and stealing a Super Force Metal. Part 2 comes along, there is another Super Force Metal to steal and you get to actually try to win.
The party issue...you CAN NOT, and I mean CAN NOT have X, Zero, and Axl in the first part because Hyper Modes are NEEDED to survive or else you will get fucked over by statuses. Marino is needed in both parts to steal the Super Force Metal. But wait, there's more...you have 6 characters in the party due to a certain plot twist, how nice. That means that in order to efficiently use Marino in part 2 to steal, you need to have Gain Hypers in your inventory which are easy to find. And Part 2 is no pushover, you need to beat the Super Force Metal on Great Redips in order to efficiently deal damage (or else he can heal and the Super Force Metal can also attack you), which means it's not just attack said boss like in most RPGs.
Then there are the statuses. Deux Ex Machina can inflict EVERY status in the game on all characters. The ways to avoid getting the statuses? Force Metal, Hyper Mode, and getting lucky.
And before you say "So it's all statuses?", Great Redips isn't a pushover when it comes to damage either. It's basically a fight that runs completely on luck, and even when you are prepared you can lose easily.
I've had less trouble with BFA in FFX, Sephiroth in FFVII, hell even the final boss of KH when I didn't know what I was doing.