I think everything pre-FFVIII was just difficult on your first encounter, but designed to doable after certain amount of grinding.
Even Omega and Shinryu from FFV could be completed once you had the key jobs leveled.
However omega weapon from FFVIII is not duable if you don't understand the correct strategy (don't get me wrong, it isn't difficult once you know what to do) but it was the first monster that required a strategy even with the best gear/stats available.
After that the progression has scaled both in complexity and time requirements, now is not just about knowing the strategy but also reaching the necessary gear/stats to execute it.
Although difficulty should also take resources into account, in the 80's it was game magazines, then came the internet, and now you just watch a video in Youtube and know exactly what to do.
With all that in mind, I think the hardest boss in FF history has been Asura from FFIV.
She is a summon that you can obtain for your party, but her specialty is healing magic, she does 2 things during the fight, auto-attack and heal herself, IIRC you reach there around lvl 35 and your party would have to be at least twice that level to out-damage her heals.
Your only real option is to know the strategy which involves a spell called "Barrier" which basically grants a reflect effect, you have to cast it on her so her healing magic cures your party instead of herself, the problem with that is that Barrier is the first installment of that kind of spell in the final fantasy franchise (at least in Western hemisphere), and your healer does not have it by the time you reach that point in the story.
She is an optional boss so most people just ignored her and kept going with the story, your only shot at the fight is keep leveling and pay attention to your spells, once your white mage learned "Barrier" the tool tip would be your only clue to take her down. And in fact it is very valuable knowledge as "Barrier" becomes a key spell for other fights in the game.