If you twink ninjas out they are probably the most overpowered class in the game outside a caster with Math Skill.

By mid way through chapter 3 you can get a +2 PA armor and hat, giving a ninja about 14 PA total. With 97 Br, 14*14*2=392 damage per hit, as a base line. After this you could equip Martial Arts to bring the total to 588, a bracer to bring it to 578, or both to have your lv30 ninja do 867 damage.

If you want to twink out for mobility you can equip Germanias Boots and Move +3 to give a ludicrous move of 8 and jump of 5, all while still being able to one shot anything that awaits you when you get there.

Survivability, as you mentioned, is the main weakness of the ninja. Once your ninja one shots everything it touches the picture changes a little bit, since you don't have to worry about counters or having them attack you back next round. Additionally the game possesses some very powerful defensive abilities, namely Blade Grasp and MP Switch. We all know how awesome Blade Grasp is, seeing as it reduces 80% of the damage you are liable to take in the game to a scant 03% chance to hit.

Lesser known is the power of MP Switch. Since ninjas have such low hp, the total mp is usually consumed on each hit, however with Move MP-UP you regenerate a token amount of MP each time you move, meaning you would get one free hit every turn. And if you are setting up any of your characters to get pile driven with multiple attacks every turn, I don't think its the classes you are using that’s the problem.

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So ends my defense of the mighty ninja. As for my vote for useless classes, I'm going with Calculator (obviously) and Samurai.

The reason I list Samurai is that other than the skills you can learn from them (which are quite good) the class itself has little use. Weak physical attack, no shield and an action command that doesn't see its full strength unless equipped on a magic class. Other than to learn the skills there is really no reason to every use them. (unless you want to take advantage of the sword from Deep Dungeon since you only have a limited supply of uber weapons).