I'd look into making your ninja an "Unchained Ninja". There's some debate on whether it's legal, but its not unreasonable to give a ninja the same updates that rogues got since it's just an archetype.
Basically you'd get the Finesse Training, Debilitating Injury, and Rogue's Edge abilities. You can check it out here.
This will free up a feat (you get weapon finesse for free, on top of dex to damage at level 3).
Also, you might want to swap your Int and Con. At a d8 hit die and 10 constitution, you'll be pretty feeble and ninjas get plenty of skillpoints already.
Here are my suggestions for ninja tricks:
2 - Combat Trick (assuming you're keeping this one)
4 - Vanishing Trick
6 - Fast Stealth
8 - Shadow Clone (Prereq for Shadow Split)
10 - Invisible Blade (too good to not get at level 10)
12 - Shadow Split (Going for the whole 'misdirection' thing you wanted)
1. Don't TWF.
2. Tell your Investigator buddy not to go with Weapon Finesse! Medium Armor proficiency and good STR/DEX is a much better way to go in my opinion, since Investigators can really benefit from the damage from a good 2H Power Attack with a Greatclub if need be (or, if you play a race with racial weapon proficiencies, any of those).
3. I honestly would consider using the Unchained Rogue instead of the Ninja, simply because of the novelty and the free Finesse and Finesse Training. For archetypes... get the Sczarni Swindler archetype! They get several nice features out of high CHA, and you can easily qualify for Eldritch Heritage (Rakshaza) for lots of tools to lie through your teeth.
4. You can go for Eldritch Heritage (Rakshaza) with a Ninja too, but the feats you will spend on Finesse make it harder for you to properly benefit from it. Maybe if you go with the Katana Power Attack build... you have less AC, but you'll probably have Shadow Clones and Invisibility so it's gonna be hard enough to hit you already.
1. Don't TWF.
2. Tell your Investigator buddy not to go with Weapon Finesse! Medium Armor proficiency and good STR/DEX is a much better way to go in my opinion, since Investigators can really benefit from the damage from a good 2H Power Attack with a Greatclub if need be (or, if you play a race with racial weapon proficiencies, any of those).
3. I honestly would consider using the Unchained Rogue instead of the Ninja, simply because of the novelty and the free Finesse and Finesse Training. For archetypes... get the Sczarni Swindler archetype! They get several nice features out of high CHA, and you can easily qualify for Eldritch Heritage (Rakshaza) for lots of tools to lie through your teeth.
4. You can go for Eldritch Heritage (Rakshaza) with a Ninja too, but the feats you will spend on Finesse make it harder for you to properly benefit from it. Maybe if you go with the Katana Power Attack build... you have less AC, but you'll probably have Shadow Clones and Invisibility so it's gonna be hard enough to hit you already.
Eldritch heritage is a good thought, but two weapon fighting should work decently well as a ninja.
The -2 to hit should be mostly offset by flanking and later being invisible all the time. More attacks is good for when you have a high damage bonus on each attack (sneak attack).
Two handing a katana is definitely a good alternative, but dual wakizashis is fine.
I agree with everything both of them said except, Secret Wizard's first point.
2x Wakazashis > single Katana when you have damage that adds to every attack.
Also, Eldritch Heritage could be good for such a character. I might suggest taking a look at other bloodlines as well though. You may also want to consider Shadow.
You want to elude notice, here's a selection of gear to get. Daggers are easily hidden, get a couple of those and shurikens. Hide Shuriken in pocketed scarf. use Tube Arrow Shooters up your sleeve. use liberally, no mention of limit so that's up to your GM. Get a bonus to being hid. Don't bother to hide one dagger. Always best to have an easily drawn blade and most people would have one. Buy masterwork quarterstaff, define masterwork as gnarls and knots carefully carved into ideal dimensions to distribute weight evenly, end result, s!*@ty looking walking stick that is a superb weapon. Upgrade as needed. Also, depending on level. Get Travelers any tool and silk rope. Silk can be used to accentuate your outfit and easily hidden, travelers any tool becomes most tool. Like for instance a grappling hook. Have fun.
EDIT: Also, poison sand tube disguised as scroll tube, packed with poisoned gunpowder.
Mithral shirt had the same AC as a regular chain shirt. Just a better dex bonus and acp.