The main storyline wasn't too hard for me. like all FFFs it has a couple of difficult ones Like Elder Wyrm, that big plant thing, and Hashmal.
I think I did die against Cid, and the first Judge quite a few times on my first playthrough. It might have been a while for some of use so we might not remember everything that might have been hard. Now that i recall I found those crystal bug things that disguise themselves as save points to have been hard.
They can piss you off especially if you've struggled a long way through that dungeon and your party has low health and when you see it you think its a lifesaver but when you come to it and try to use it, you're hit by blizzaga.
the later hunts get especially hard like when you journey into the Penumbra. I gave up there after repeatedly dying after walking around for about 8 secs before being mauled by a pack of bull frogs and blue horses.