This shit always made me wonder. FF3 is a prime example.
You get 5 batches of jobs, one from each crystal and another near the end with the two uber classes. You get the first batch near the beginning of the game, and you don't get the second until nearly halfway through the fucking game. It's immediately followed by the third batch, then you don't get the 4th batch until right before you get the uber jobs. Shaman and Warlock are the upgrades to White Wizard and Black Wizard respectively, but you don't get them until 1-2 bossfights before you get the Sage class that makes them completely worthless. Why these classes weren't in the 2nd batch of jobs along with the Knight and Karateka jobs(physical class upgrades), I will never know. Why the job batches aren't better spread out instead of dumping the majority of them on you after half the game is done, I will never know. At least they did a better job of spacing the jobs out with 5, and making the job system more useful than "switch everyone to this class for this boss fight/area". That's just the job system issue, that doesn't even take into account entire sections of the game where the recommended strategy is "run away from everything, they are all too powerful at your current level".
Mother is a directionless mess on it's own level. Switching between tight corridors and wide open areas at random, enemies that vary wildly in difficulty in the same area, and adding and removing party members making you either painfully weak or absurdly overpowered for the area you are in. A good portion of the game is sitting around and grinding up another 5-10 levels when reaching a new area, just so enemies stop being able to one-shot you. At least what I've played of it. I got tired of it somewhere EVE.