Okay, so in the spirit of the Hexblade and the Knight, I've also worked on the Ninja a bit. Ninja
Hit Die: d6
Important Stats: Dex>Int>Wis>Con>Cha>Str
Class skills: Balance, Climb, Concentration, Decipher Script, Disable Device, Disguise, Escape Artist, Forgery, Hide, Jump, Listen, Move Silently, Open Lock, Perform, Search, Sense Motive, Sleight of Hand, Spot, Survival, Swim, Tumble, Use Magic Device, Use Rope.
Skill Points Per Level: 8 + Int modifier
|1st||+0||+0||+2||+0||Ki Power (Will saves), Sneak Attack +1d6, AC Bonus +0, Trapfinding|
|2nd||+1||+0||+3||+0||Ghost Step (Invisible)|
|3rd||+2||+1||+3||+1||Sneak Attack +2d6, Poison Use|
|4th||+3||+1||+4||+1||Evasion, Great Leap|
|5th||+3||+1||+4||+1||Ki Power (Mettle of Will), Sneak Attack +3d6, AC Bonus +1|
|6th||+4||+2||+5||+2||Acrobatics +2, Ki Dodge 1/encounter|
|7th||+5||+2||+5||+2||Sneak Attack +4d6, Speed Climb|
|8th||+6/+1||+2||+6||+2||Great Acrobatics, Trackless Step|
|9th||+6/+1||+3||+6||+3||Ki Power (Force of Will), Sneak Attack +5d6, Improved Poison Use|
|10th||+7/+2||+3||+7||+3||Ghost Step (Ethereal), AC Bonus +2, Ki Dodge 2/encounter|
|11th||+8/+3||+3||+7||+3||Sneak Attack +6d6, Ghost Strike|
|12th||+9/+4||+4||+8||+4||Improved Evasion, Acrobatics +4|
|13th||+9/+4||+4||+8||+4||Ki Power (Mind Blank), Sneak Attack +7d6|
|14th||+10/+5||+4||+9||+4||Ghost Sight, Ki Dodge 3/encounter|
|15th||+11/+6/+1||+5||+9||+5||Sneak Attack +8d6, AC Bonus +3, Master Poison Use|
|16th||+12/+7/+2||+5||+10||+5||Ghost Mind, Hide in Plain Sight|
|17th||+12/+7/+2||+5||+10||+5||Sneak Attack +9d6|
|18th||+13/+8/+3||+6||+11||+6||Ghost Step (Superior), Acrobatics +6, Ki Dodge 4/encounter|
|19th||+14/+9/+4||+6||+11||+6||Sneak Attack +10d6|
|20th||+15/+10/+5||+6||+12||+6||AC Bonus +4, Superior Evasion|
Weapon and Armor Proficiency: Ninjas are proficient with (insert list), light armor, but not shields.
Ki Power (Ex): Ninjas hold an inner ability referred to as Ki. A Ninja's Ki strengthen's as it levels up in the following ways:
* At 1st level, a Ninja gains a +2 bonus on Will saves, due to its Ki.
* At 5th level, a Ninja gains the Mettle ability, but only for Will saves.
* At 9th level, a Ninja no longer fails will saves on a roll of 1. In addition, a Ninja gains the slipper mind feature, as a Rogue.
* At 13th level, a Ninja's ki power purifies its mind. The ninja becomes immune to mind-affecting effects.
Sneak Attack (Ex): A Ninja gains 1d6 sneak attack at level 1, and increasing sneak attack dice as the chart above indicates.
AC Bonus (Ex): While wearing light or no armor, a Ninja may add his Wisdom bonus to his Armor Class. This ability functions like the Monk's AC Bonus and does not stack with the Monk or Swordsage's AC Bonus.
Trapfinding (Ex): A Ninja gains the trapfinding ability.
Ghost Step (Su): A Ninja can, as a swift action, activate his Ghost Step ability. A Ninja can use his Ghost Step ability a number of times per encounter equal to 1/2 his Ninja levels + his Wisdom modifier. Each use of his Ghost Step ability lasts for 1 full round.
* At 2nd level, a Ninja can turn invisible with his Ghost Step ability.
* At 10th level, a Ninja can turn ethereal with his Ghost Step ability. He may still choose to turn invisible instead, if he desires.
* At 18th level, a Ninja's Ghost Step acts as Superior Invisibility in addition to turning him ethereal.
Poison Use (Ex):
* At 3rd level, a Ninja never risks accidentally poisoning herself when applying poison to an object.
* At 9th level, a Ninja can apply poison to a weapon as a move action.
* At 15th level, a Ninja becomes immune to poisons of any kind and may apply poison to a weapon as a swift action
* At 4th level, a Ninja takes no damage from an effect that allows a reflex save for half if he makes the save.
* At 12th level, a Ninja takes only half damage from an effect that allows a reflex save for half if he fails the save.
* at 20th level, a Ninja takes no damage from any effect that allows a reflex save.
Great Leap (Ex): A Ninja gains the Run feat and may always make jump checks as if he had a running start.
Acrobatics (Ex): A Ninja gains a bonus on Balance, Climb, Jump, and Tumble checks as indicated on the chart above.
Ki Dodge (Su): Beginning at 6th level, a Ninja may, once per encounter, focus her Ki Power to allow her supernatural reflexes. Activating Ki Dodge requires a swift action and lasts for a number of rounds equal to 3 + Ninja's Wisdom modifier. At 6th level, the ability grants a 20% miss change to the Ninja. This miss chance is not concealment, and will not negate precision based damage. At 8th level, and every 2 levels thereafter, the miss chance increases by 5%, to a maximum of 50% at 18th level. A Ninja gains additional uses of this ability as indicated on the table above.
Speed Climb (Ex): A Ninja becomes so adept at climbing, that she gains a climb speed equal to her land speed.
Great Acrobatics (Ex): A Ninja is so dexterous that he may use his Dexterity bonus in place of any Strength bonus for all skills.
Trackless Step (Ex): A Ninja leaves not trail and may not be tracked. He may leave a trail if so desired.
Ghost Strike (Su): At 11th level, any armor worn by the Ninja and any weapons wielded by the Ninja are under a constant Ghost Touch effect. This effect ends 1 round after the item leaves the Ninja's possession.
Ghost Sight (Su): A Ninja can see invisible and etheral creatures and objects as easily as he can see material creatures and objects.
Ghost Mind (Ex): Anyone attempting to use a Divination spell to locate/observe/learn about the Ninja must succeed on a caster level check (DC 20+ Ninja's class level) or the effect fails. Effects that observe an area do not fail, but the Ninja is not detected if the caster level check is not successful.
Hide in Plain Sight (Su): As the Shadowdancer's HiPS.
One thing to note is that I'm a believer that you need X minutes of down time between encounters to refocus your mind/catch your breath/etc. So whether X is 5 minutes in your game or 15, know that you can't just start/end encounters at will to stay invisible forever.
Tome of Battle has established the normal downtime at 5-minutes, and I think that's a solid starting point. After all, any round/level buffs will be over by that point.