So Sudden Strike-
One fix is for it to do d6 against flatfooted opponents, and d4 against flanked. However, this is still worse off than sneak, and the class features the ninja gets doesn't even compare to what a rogue gets (and rogues aren't that powerful). I say, d8 flatfoot, d4 flank. Is that too powerful?
Another idea I had for them was to give them a riposte- sort of like the alt feature for scouts in Cityscape. If a foe attacks the ninjer and misses, he's flatfoot till the end of the ninja's turn. At some higher level, he can take a single attack on a foe that misses him. I think this might be really powerful... maybe if they miss AoOs...
Also, the damn well need more ki powers. Something that gives them versatility.