Human Ninja all the way
your skills should reflect how you want him to play, is there another rogue in the party? thats nice, max out balance and tumble and jump, be a ninja, they were stealthy and moer agile than some common thief
feats?
if you focus on melee, anything that helps helps
toughness is always good, mainly at low levels atleast
but ninjas, well speed... dodge boosts your armor, take enough ranks in tumble and start fighting defensivly and you never get hit (cept for that rare time you do and its a fire giants, and he crits you, and you die..yeah, bad memories) then take mobility, good for moving through people, but it opens up spring attack, over looked because of its requirments, but being able to move, strike, and move again, its pretty ninja
also, focus on a single attack destroying a foe
sure, twf is nice because who doesnt like having two weapons? but you only apply sudden strike on one attack, this is where power attack comes in
only one attack? MAKE IT COUNT! with an enemy already denied dex bonus, you can hit easier, so power attack can really mess people (or monsters) up, and if you are a human, perhaps take a very un-ninja weapon, you get an extra feat after all, exotic weapon proficeny with teh bastard sword can make you deadly (remember, a katana is a masterwork bastard sword, so it makes sense) or even the kursu-gama, it doesnt do much damage, but it has reach
now onto a more importantly overlooked part of ninjas, poison use
this, if done right, keeps the DM on their toes, applying poison takes a round, but if you apply poison and not use the weapon for a few rounds, they forget, then you can destroy your foe
and lastly, your KI ability, stay ninja, you get cooler uses and with the right feats they put the paladin's smite to shame