Suikoden II - One of my favorite RPGs for the PS1, it would be THE favorite but for one thing:
The meta-game of collecting all the stars of destiny. While I don't think this game was as brutal about it as some of the other Suikoden games, if you want the best ending you pretty much go in with this checklist of who to talk to when and with what prerequisites checked. I absolutely loved the concept of the growing castle, and collecting all the stars of destiny but up until that point instead of just enjoying the game it felt kind of like running errands, just doing busywork to ensure I'd have to do less busywork once I got to the actual castle.
Legend of Mana I had a similar issue with to a lesser degree, though it's more convoluted. If you really want to maximize your playthrough, you have to figure up artifact distance from your home, proper spirit levels to get the kinds of results you want, and a bunch of other micro-managing nonsense behind the scenes, fortunately most of it plays no impact on the story so it's easier to ignore.
Final Fantasy XII, I loved most everything about this game EXCEPT for 3 things:
1) The ridiculous trial-and-error boss difficulty that often required specific buffs/debuffs to be cast and managed with no clear indication of what those were.
2) The way some really awesome items, which you could waste an entire license on were hidden in arbitrary chests that let RNGs determine whether you even got the item or not, even if you're aware it's there from a guide, you have to save SCUM A LOT just to get the item (I'm sorry but reloading the game 30 times doesn't spell out to me "50% chance")
3) The license board, it was a cool feature, and at first it let you customize characters to a degree, but around level 40-50 pretty much every character's license board was filled out making everyone an interchangeable hybrid. I would have much preferred specialized characters or a job class system.