My rework is centered around removing study and assassinate. In exchange, ninja receive a generic melee boost with a couple of utility skills thrown in. Then we add new ninjutsu paths. Keep in mind that while ninja here get a relatively powerful skillset, they are limited by racial stats, size, hp, etc.
The Shinobi (spy) path is the stealth and survival path. They will play much like maledictive thieves, being pure rogues. They are particularly hard to surprise and finish off.
The Boryaku (strategy) path is the utility path. They fight well outdoors and can track you. They use the environment and active skills to gain an advantage.
The Keiri (executioner) path is the combat path. Closest thing to a straight fighter. They are adept at killing other rogues with their weapon selection and their counters give them a blademaster feeling.
All ninja:
Disguise
+10% exotic max prof
+3% sword max prof
+3% dagger max prof
First parry (monk)*
Second parry (monk)*
Martial arts b*
Martial arts a*
Kickboxing b*
Kickboxing a*
Weaponlock immunity
Offhand disarm
Sense movement
lose assassinate
lose death kiss
lose falcon eye
lose study
lose lotus scourge
lose ikuzachi
*unarmed fighting skills are mostly for flavor: they aren't very effective without beads, stances, or anatomies---the unarmed parries might be useful sometimes though---for example when using a net (new ability).
Shadowstrike/doublesheath are worked into the paths.
Shinobi (Spy path)
Immune to ranger/ninja track, cabal 'spy' and other location/tracking/gate in abilities.
Autosneak
On deathblow, final attack hits decoy (if timer is not running) and ninja auto-flees (regardless if decoy fired or not, ninja avoids attack). 672 hour cooldown.
Can hide at night (6 pm to 6 am) anywhere with a 2 tick cooldown, but any movement while hidden takes you out of shadows: similar to old 'fade' skill, but detectable with detect hidden.
Can open, close, pick, and lock doors while hidden. If done while hidden, local echo of door movements is hidden on both sides of the door.
Edge darts instead of shurikens. Darts do 25% less damage than shurikens, but can have different maledictive/mental effects (think of archery ranger projective effects except through manual throw)
Heresy - Like gag, except only works on communers. Can only use on sleeping targets.
Stab - Like a single backstab, except can wound and can cause bloodloss. Penalty to hit if target is awake; greater penalty to hit if target is awake AND ninja is not hidden. Target current health is not considered.
Agent - Puts an invis/camo/hidden watcher mob that reports yells and in room actions to the ninja. Only one at a time.
Doublesheath
Boryaku (Tactical path)
Tumbling - (prof/2) chance for 'balance' if hit by a lag attack - means you take damage, but no lag.
Meteorology - Predicts upcoming weather changes. Gains an extra attack and +(level/10)% dodge in poor weather outdoors.
Geography - Hide in shallow/deep water, dodge fired weapons/thrown items in forest, autokick in plains, grapple/trip effectiveness increased in swamp, two tick dirt kick in desert, +2 mal level dust/smoke in air, else other outdoors: +2 avg damage per strike.
Track (Ranger)
Fireworks - Area flashfire/thunderclap (save for each)---does minor damage (therefore wakes enemy). Has 2 tick cooldown.
Net - Out of combat: creates a net (3 tick cooldown on create, lasts 24 ticks). In combat: throws the net for an attempted short-term entangle effect. Must be holding the net in a hand to throw it.
Traps - Places a shuriken, net, caltrap, or firework trap at an exit or object. Shuriken/net requires the item and expends it. Fireworks must not be on cooldown and sets the skill on cooldown. Caltrap trap hits flying enemies normally. Shurikens deal damage and can poison. Firework trap spells have +2 level compared to ninja.
Backcutter (all weapons)
Keiri (Executioner path)
Polearm
Pugil works with polearms and spears
Two handed
Dual parry
Counter
Double counter
Iaijutsu - counters strangle/blackjack and ninja opening 'murder' cannot be countered. Iaijutsu triggering against iaijutsu means defender counters then attacker counters then defender double counters.
Blind fighting
Chii adds +5 hit/dam
+1 size when grappling
Mounted combat
+2% staff prof
Shadowstrike