I won't make this another super megathread with like thirty posts. Just this one. Let's keep it clean and simple.
The ninja is a rogue alt-class that keeps the rogue chassis and exchanges a few abilities. Overall, I think it works pretty well - you can see the "rogue" inside the ninja, while at the same time seeing how there's differences. In total, the rogue loses trapfinding for poison use, and changes the evasion tree for Light Steps / No Trace. The ninja also gains a ki pool which gives it a boost over the rogue, which is required for some talents - which helps balance it out, since rogue talents are basically "whenever I want."
So trapfinding for poison use works well...in theory. The issue here isn't with the ninja, to be fair, but rather with how poisons work - a problem that has been most apparent since the alchemist came out. If something can be hashed out for crafting and for poisons, I can see this trade as a really good - and altogether fair - one. My hope is for new poisons to make an appearance in the book.
The other trade off of evasion for Light Steps / No Trace also works. Both the abilities are p. dang flavorful, fitting the vague "mythos" of the ninja as seen in the west. It's an interesting comparison - the ninja loses some out of combat (trapfinding) foor some in combat (poison use), then loses some in combat (evasion) for some out of combat (light steps / no trace). I actually really like the exchange - it feels like you're losing something of worth and gaining something of worth in both cases.
The other main change is talents/Ki Points. Now, I've already railed against unrechargable ki points elsewhere, so I won't do it here. It's a bit of a change to have it based on charisma instead of wisdom, but I think I can see why - ki points and wisdom are sort of the monk's "schtick," and the charisma serves the ninja rather well. Beyond that, charisma is implied as the mental version of strength - inner power over one's surroundings, as archtyped by spontanious, less "learned" casters - which rather fits the theme of ninjitsu. Overall, I can see the argument for charisma over wisdom.
I won't go through each and every trick - just the ones that stand out. Ki Block is way, way too specialized. Ki Charge might have it's damage brought up a bit, but it seems mostly useful for out of combat stuff (there's always a reason to make something explode). Every ninja will have forgotten trick, but I think that in a good way.
Overall, I like the ninja a lot. I think it's could be knocked down a bit to make the poor rogue feel better, though. Potentially give it 6 + int skills rather then 8 + int? Rogues should definately get a talent / master talent that lets them choose one ninja trick / master trick, as well.
Seriously this movie is amazing.