One I haven't heard mentioned much yet (possibly because it got patched away within a few months after release) was the wonky experience system. You literally couldn't figure out how to level your character.
Well, it wasn't so much that you couldn't figure it out, is that it was entirely random.
OK, first off, I have to explain that you have two levels: your character level and your class level. Your character level would slowly go up by getting regular old XP. Your class level involved getting "SP" and SP was randomly rewarded by doing actions related to the class.
And I mean that literally. Using a class's action had a random chance of gaining SP, depending on the level of the target the action was being used on.
Now you might assume based on what I just described that "character level" was like a traditional RPG level and that "class level" would be used to unlock skills or something. Nope. All the "character level" did was unlock attribute points you can use to increase attributes whose meaning was never explained. The "class level" was your traditional RPG level - increasing it would increase all your attributes on a set growth curve. (In addition to being used to unlock skills.) And leveling that up was, quite literally, random.
The random factor was what was patched out a few months after release, they changed it so that killing enemies always generated SP. As far as I know, they never got rid of the "character" level, whose sole purpose was granting "bonus" attribute points.