Two immediately come to mind.
Story gripes; Final Fantasy 8. I Dropped that game like a bad habit. I was putting up with the god awful junction and magic draining system. The story started off brilliantly! Loved it. But as it carried on, it got worse and WORSE. Eventually, There was a flash back scene where you learned everyone knew each other from their childhood, and it was really the last straw. I got up, turned my PS1 off, and did something else.
Gameplay; FF8 also almost wins this one for the draw system required for junction. GRR. But no. I bought Terminator Salvation for 10 dollars. For that price, it's not a bad buy. I mean, the game still sucks. But at 10 dollars, it's like a steal DL game... on disk.

There are sections of the game called "Rail" sections. You're in a vehicle, manning some gun. When I started, level 2 was an escape section on a jeep or some such, and you had to take down these fliers and eventually an HK (Hunter Killer iconic air unit from the movies) in steps. It's really easy to fail for some reason. I wanted to strangle whoever designed the game levels. Some of the rail sections are unlikeable, unbareable, and nearly unplayable. I nearly gave up.