Razjah
Explorer
I would embrace the koboldishness and make this guy a master of all thing traps, especially setting them. It's something that probably hasn't been done at your table before and has a very different feel from other characters.
There is a ranger archetype that can make traps instead of getting spells. The class can make mechanical traps with supplies or supernatural traps with the substitute magical ability. It also gets trapfinding as a class feature. Possibly worth looking into.
Back on the original topic:
I went over the Ninja class slower, it does seem like a fun class. I'm no optimizer, but it looks like a player could have fun with it.
What stats do the party get? 15 point build, 20? Rolled stats? The strength penalty really doesn't matter that much with the sneak attack damage and magic weapons. Weapon Finesse alone should really help the ninja. Later one a simple +2 strength item can help later if the player is really worried about strength effecting damage.
A starting 10 Str will drop to a 6. This is still only a -2 to attack damage. The sneak attacks, twf, and magic should be more than enough for damage. In Pathfinder weapon finesse can be taken at level 1, there is no +1 BAB prereq anymore.