IV - Prolly the final dungeon, encounters take too damn long.
V - Gonna agree with Wolf Kanno on the beginning of the game up until the Library.
VI - Vector and the Magitek Lab. Drags on too much.
VII - Costa Del Sol up until Cosmo Canyon. I don't particularly enjoy the Corel train trek or the Desert Prison.
VIII - D-District Prison, duh.
IX - I think Mt Gulug was when things started to drag a bit much.
X - Mount Gagazet. It just goes on for too long and it's sandwiched between some of my favorite parts of the game.
X-2 - Chapter 4 CommSpheres *shudder*
XII - Tchita Uplands and Sochen Cave Palace. By the time they roll around I'm just kinda done with the trek to Archades and want to be there already.
XIII - Heh.