For a series with cult status it sure exhibits a lot of flaws. The one that gets me the most is that they use unskippable cutscenes all over the damn place; if I'm going to have to grind through a bunch of monsters to get my party up to the appropriate levels, then I don't really want to have to sit around and wait for my characters to jump up and down when they level up and so on. The credits sequence after the first half hour of gameplay actually had me thinking that the game had ended and that I'd paid GBP30 for 30 minutes...
Anyway. One thing that I was thinking about this morning is the job system. Jobs - better knows as character classes - determine a bunch of things, apparently. You only have four people in your party, but there are many more jobs than that, so you find yourself training each character up in multiple jobs and then switching between them according to what the situation demands. It's quite a nice idea, but what bugs me is the way in which each job is trained entirely independently; switching my high-level white mage to red mage sees her starting her training from scratch, and that's not terribly believable.
I can see that they wanted to have you incur some kind of penalty for switching jobs, but I think it would have been nicer if they'd dropped the 'training up your job level' idea and just based the whole thing on character stats instead. Gaining lots of XP as a warrior increases your Strength and Endurance base stats. Gaining lots of XP as a mage increases your Intelligence, etc. Then, the 'job level' is actually just something calculated from your base stats; you could end up with a high job level for a job you've not ever actually used, but that kinda makes sense, because you'd expect a proficient white mage to be at least a reasonably competent red mage. It would allow 'sideways' movements in jobs while still preventing people from completely changing course.
It almost turns the job system into "which stats should I raise now?" except that there are other things keyed from it too, like usable equipment types or special abilities, so that makes it a bit more interesting.