Just a hint, never invest points in Combat skills like Hand & Feet. If your Ninja is attacking with punch or kick that skill will rise automatically by use. Until Ninjutsu skill is fairly decent {50-60 points} Ninja are good to keep in back row. Hide skill allows them to sneak around and attack with (s)hort range weapons like their knuckles and heels. Seeing as how their primary skills are Ninjutsu and Hand & Feet, early on this approach builds those skills up fairly quickly, leaving level up points {sometimes Ninjas get none} for other skills like skullduggery/alchemy/kirijutsu or w/e.
Later, a Ninja can be deadly on the front line, their class speed and Ninjutsu based armor class can end up making them the best defensively in your front line members. Once they are front line you will most likely have come across some interesting weapons they can use, and sometimes only they can use (note:Faeries are unable to wield most normal sized weapons-but they get their own weapons). By that time also, you would most likely be able to level a weapon skill from zero without too much fuss through random encounters. Either Hide the rest of the party once they have neutralized the enemy w/ sleep/hold monster/etc. or parry dodge everyone and let the Ninja chop them up w/ new weapon(s). Result: fast weapon skill ups.
I've been keeping a Ninja on front lines and she rarely gets damaged except from AOE spells/breath weapons. For armor just a shadow cloak and she has -3 Armor Class which is better in every slot than my Valkyrie or Lord....