All the worst things...
There are parts of rpgs that suck...
the storyline and narrative aspects are good, but why did you put ff style fight scenes in!? I guess it would be *just* bearable if you did them at a pace which was at least half the speed of a normal ff battle.
Hell! the stupid "battle!!" thing (please NEVER do it again) took 3 seconds to go across the sceen and looked really bad... not just bad, it raised a new standard of looking shit.
Most of your sound loops weren't that good, the horrible "used for every door and portal" sound effect is still irritating me now.
Also why is zack 4 times the size of everyone else? and why does he have only 2 frames of animation?