I don't tend to revisit games I didn't like the first time, as I find that there are too many interesting new games I haven't played yet for me to spend time giving second chances to things I didn't already enjoy. So I'm not sure there are any Final Fantasy games that precisely fit the bill for me. Still, there are definitely a couple where I've found that certain things have derailed multiple replay attempts, even if I otherwise really like them.

Firstly, I absolutely hate the desert prison in FFVIII. A contender for the outright worst FF dungeon, in my opinion, and one that has killed off multiple replays for me in the past. It doesn't really help that it comes right on the back of the parade at the end of disc one, which is easily one of the high points of the entire game. If I drop a run of Final Fantasy VIII, it's pretty much guaranteed to be at that point, and it's the only thing that has deterred me from revisiting the game more frequently than I have.

Secondly, I've never been able to make it more than a few hours into Final Fantasy V on any of my replay attempts. It's not exactly the fault of the game, but something about the job ability system compels me to want to unlock everything, and I find that it quickly becomes overwhelming, and slows my progress to a crawl. It was okay on my first run, when I was a kid and had loads of time to grind out things like Dualcast, but I don't think I'm ever going to finish it again unless I learn to be okay with not unlocking all the abilities.

Also, maybe a slightly controversial opinion, but I never really liked the World of Ruin very much in FFVI. I admire how bold the concept of it is, and certain individual scenes in it are very memorable, but on the whole I always found it kind of a drag to play compared to everything that comes before it. I've played VI up to that point five or six times, but I think I only ever finished the game once.