Here's doing it as a 20 level base class...
Ninja (base class)
HD: d8, BAB: 3/4, Saves: good Reflex, Skills: 6 + INT modifier
SKills: Acrobatics, Bluff, Climb, Craft, Disable Device, Disguise, Escape Artist, Intimidate, Knowledge dungeoneering, Knowledge history, Knowledge local, Linguistics, Perception, Profession, Sense Motive, Sleight of Hand, Stealth, Swim, Use Magic Device.
Ninja are proficient in all simple weapons, plus the kama, katana (bastard sword), kukri, longsword, nunchaku, sai, scimitar, short sword, shuriken, siangham, Ninja are not proficient in any armor or shields.
1st: AC nonus, ki pool, Ki reserve power, sneak attack +1d6, trapfinding
2nd: Evasion, Talent
3rd: Sneak attack +2d6, poison Use
4th: Talent, +1 AC
5th: Sneak attack +3d6
6th: Talent
7th: Sneak attack +4d6
8th: Talent, +2 AC
9th: Sneak attack +5d6, improved poison Use
10th: Advanced talents, talent
11th: Sneak attack +6d6
12th: Talent, +3 AC
13th: Sneak attack +7d6
14th: Talent
15th: Sneak attack +8d6, greater poison Use
16th: Talent, + 4 AC
17th: Sneak attack +9d6
18th: Talent
19th: Sneak attack +10d6
20th: Ultimate talent, talent, +5 AC
AC Bonus. When unarmored and unencumbered, the ninja adds her Wisdom bonus (if any) to her AC and CMD. This applies to her touch AC and when she is flat-footed, but not when she is immobilized. At level 4, and every 4 levels thereafter, this bonus increases by 1.
Ki Pool (Su). The ninja has a reserve of mystical energy called her ki pool. It has a number of points equal to ½ her class level plus her Wisdom bonus. As long as she has at least 1 point in her ki pool, she has access to her Ki Reserve Power. By spending 1 point from her ki pool, a ninja can make 1 additional attack at her highest attack bonus when making a full attack. In addition, she can spend 1 point to increase her speed by 20 feet for round. Finally, a ninja can spend 1 point from her ki pool to give herself a +4 dodge bonus to AC for 1 round. Each of these powers is activated as a swift action. As a ninja gains levels, points from her ki pool can be spent to activate many of her Talents.
Ki Reserve Power (Su). At 1st level, the ninja chooses one of the following Ki Reserve Powers. As long as she has at least 1 point in her Ki Pool, she has access to her selected Ki Reserve Power.
Damage Reduction. The ninja gains DR/magic equal to ½ her level (minimum 1).
Enduring Fortitude. The ninja gains the benefits of the Endurance and Diehard feats. In addition, she adds half of her ninja level to the bonuses provided by the Endurance feat.
Energy Resistance. Choose 1 energy type (acid, cold, electricity, fire, or sonic). The ninja gains resistance 5 to the selected energy type; this increases by 5 at level 4 and every 4 levels thereafter.
Inner Strength. The ninja adds half her level (minimum 1) to her Will Saves.
Inner Fortitude. The ninja adds half her level (minimum 1) to her Fortitude Saves.
Light as Air. The ninja benefits from a constant feather fall effect. At 6th level, she gains a constant water walking effect. At 12th level, she gains a constant air walk effect.
Mystic Celerity. The ninja’s speed increases by 10 feet. This increases to 20 feet at 7th level, 30 feet at 13th level, and 40 feet at 19th level.
Night Vision. The ninja gains lowlight vision (or superior lowlight vision if she already has lowlight vision). At 5th level, she gains dark vision 60 feet (or her existing dark vision increases by 60 feet). At 10th level, she gains the ability to see through magical darkness. At 15th level, she gains blind sense 60 feet. At 20th level, she gains blind sight 60 feet.
Unarmed Damage. The ninja benefits from the Improved Unarmed Strike feat and her unarmed damage equals a monk’s of the same level. Monk and ninja levels stack for the purposes of determining her unarmed damage.
Sneak Attack (Ex) as per rogue class feature.
Trapfinding. The ninja gains the rogue ability of the same name.
Evasion (Ex). The ninja gains the rogue ability of the same name.
Talents. At 2nd level, and every 2 levels there after the ninja chooses one of the following abilities.
Combat Mastery. The ninja can spend 1 point from her Ki Pool as a swift action and for 1 round gain the benefits of a combat feat that she qualifies for but does not have.
Concealment. The ninja can spend 1 point from her Ki Pool as a swift action gain concealment, including benefiting from a 20% miss chance, for a number of rounds equal to her Wisdom bonus.
Extra Class Skill. The ninja may choose 1 cross-class skill and add it to her list of class skills. This talent may be chosen more than once.
Ghost Sight. The ninja can spend 1 point from her Ki Pool as a swift action and benefit from the see invisible spell for a number of rounds equal to her Wisdom bonus.
Ghost Step. The ninja can spend 1 point from her Ki Pool as a swift action and become and remain invisible for 1 round.
Ghost Touch. The ninja can strike incorporeal targets as if they were corporeal.
Improved Uncanny Dodge. The ninja gains the Improved Uncanny Dodge ability. She must have Uncanny Dodge before selecting this ability.
Ki Blast. The ninja can spend 1 point from her Ki Pool as a swift action and for 1 round gain the ability to make ranged touch attacks with a range of 60 feet that cause damage equal to her ninja level plus her Wisdom bonus on a successful hit.
Minor Venom. The ninja can spend 1 point from her Ki Pool as a swift action and poison 1 weapon with a mystic poison for up to 1 minute per level or until the weapon successfully strikes a target. This poison does 1d3 points of ability damage of the ninja’s choice (Strength, Dexterity, Constitution, Intelligence, Wisdom, or Charisma) for a number of rounds equal to the ninja’s Wisdom bonus. The Save DC is 10 + ½ the ninja’s class level + her Wisdom modifier. A successful save prevents further damage from occurring.
Potent Skill. Choose 1 skill you are trained in. The ninja can spend 1 point from her Ki Pool as a swift action and add +20 to the all skill checks of the chosen skill for 1 round. This ability may be selected more than once, each time applying to a different skill.
Puissant Strike. The ninja can spend 1 point from her Ki Pool as a swift action and add her Wisdom bonus to her attack and damage rolls for 1 round.
Rogue Talent. The ninja can select a rogue talent. She can choose this talent more than once, each time selecting a different talent from the list available of rogues.
Second Ki Reserve Power. The ninja may select a second Ki Reserve Power.
Silencing Attack. When the ninja makes a successful critical hit or sneak attack attack, she may spend 1 point from her Ki Pool as an immediate action and cause her opponent to be silenced (as the spell, but only targeting her opponent) for a number of rounds equal to her Wisdom bonus.
Swift Feint. The ninja can spend 1 point from her Ki Pool as a swift action and may make a Bluff check to feint in combat as a free action for 1 round.
Swift Stride. The ninja can spend 1 point from her Ki Pool as a swift action and move up to her speed.
Uncanny Dodge. The ninja gains the Uncanny Dodge ability.
Wholeness of Body. The ninja can spend 1 point from her Ki Pool as a swift action and regain a number of hit points equal to her class level.
Wraithstrike. The ninja can spend 1 point from her Ki Pool as a swift action and resolve all melee attacks for 1 round as melee touch attacks.
Poison Use (Ex). At 3rd level, the ninja never risks accidentally poisoning herself when using poison. At 9th level, she gains Improved Poison Use, which allows her to apply poison to her weapon as a move action. At 15th level, she gains Greater Poison Use, which allows her to apply poison to her weapon as an immediate action.
Advanced Talents (Su). Beginning at 10th level, the following advanced talents become available whenever the ninja may select a new talent.
Abundant Step. The ninja can spend 1 point from her Ki Pool as a swift action and use dimension door with a caster level equal to her ninja level.
Crippling Strike. The ninja gains the rogue ability of the same name.
Defensive Roll. The ninja gains the rogue ability of the same name.
Dispelling Attack. The ninja gains the rogue ability of the same name.
Feat. The ninja may select any feat she qualifies for.
Flicker. The ninja can spend 1 point from her Ki Pool and gain the ability to teleport 5 feet per 2 class levels as an immediate action once per round for a number of rounds equal to her Wisdom bonus. If she teleports away in response to an attack, she gains a 50% miss chance against that attack.
Ghost Mind. The ninja gains Spell Resistance 15 + her class level against divination spells.
Hide in Plain Sight. The ninja gains the ability to use the Stealth skill to hide even while being observed, as if she had the shadow dancer ability of the same name.
Hummingbird’s Dance. The ninja can spend 1 point from her Ki Pool as a swift action and gain the benefit of a Blink spell for a number of rounds equal to her class level.
Improved Concealment. The ninja can spend 1 point from her Ki Pool as a swift action gain full concealment, including benefiting from a 50% miss chance, for a number of rounds equal to her Wisdom bonus. She must have the Concealment talent before selecting this talent.
Improved Ghost Step. The ninja can spend 1 point from her Ki Pool as a swift action and become and remain ethereal for 1 round or invisible for a number of rounds equal to her Wisdom bonus. She must have the Ghost Step talent before selecting the ability.
Improved Ghost Sight. The ninja can spend 1 point from her Ki Pool as a swift action and benefit from True Seeing for a number of rounds equal to her Wisdom bonus. She must have the Ghost Sight talent before selecting this ability.
Improved Ki Blast. When the ninja uses her Ki Blast ability against the target, on a successful hit she may use one of the following abilities as a free action that does not provoke an attack of opportunity: Bull Rush, Disarm, Sunder, or Trip using a CMB equal to the ninja’s class level plus her Wisdom bonus, or Pull the opponent a distance towards the ninja, up to the closest square that is adjacent to the ninja.
Improved Wholeness of Body. The ninja can spend 1 point from her Ki Pool as a swift action and gain Fast Healing equal to ½ her class level for a number of rounds equal to her Wisdom modifier. She must have the Wholeness of Body ability before selecting this ability.
Ki Mastery. The ninja gains the ability to spend points from her Ki Pool as a free action instead of as a swift action.
Ki Strike. The ninja can spend 1 point from her Ki Pool as an immediate action and bypass the damage reduction of her opponent.
Major Venom. The ninja can spend 1 point from her Ki Pool as a swift action and poison 1 weapon with a mystic poison for up to 1 hour per level or until the weapon successfully strikes a target. This poison does 1d6 points of ability damage of the ninja’s choice (Strength, Dexterity, Constitution, Intelligence, Wisdom, or Charisma) for a number of rounds equal to the ninja’s Wisdom bonus. The Save DC is 10 + ½ the ninja’s class level + her Wisdom modifier. Two successful saves prevent further damage from occurring.
Opportunist. The ninja gains the rogue ability of the same name.
Poison Resistance. Whenever the ninja is subjected to ability damage or ability drain from poison, she subtracts her Wisdom bonus from the amount of ability damage or ability drain she suffers.
Potent Poison. If the ninja uses poison on an attack that is also a successful sneak attack, she adds the number of sudden strike dice she has to the Save DC of the poison.
Skill Mastery. The ninja gains the rogue ability of the same name.
Slippery Mind. The ninja gains the rogue ability of the same name.
Third Ki Reserve Power. The ninja may select a third Ki Reserve Power. She must have the Second Ki Reserve Power ability before selecting this talent.
Ultimate Talent (Su). At 20th level, the ninja may select one of the following abilities in addition to the regular Talent or Advanced Talent she gets for being 20th level.
Ghost Walk. The ninja can spend 1 point from her Ki Pool as a swift action and benefit from the Ethereal Jaunt spell.
Quick Killer. The ninja can make a coup de grace as a swift action that does not provoke attacks of opportunity.
Shadow Walk. The ninja can spend 1 point from her Ki Pool as a swift action and benefit from the Shadow Walk spell.
Truly Potent Poison. If the ninja uses poison on an attack that is also a successful sneak attack, she adds her sneak attack damage to the save DC of the poison.
Truly Puissant Strike. When the ninja makes a successful critical hit or sneak attack, she may spend 1 point from her Ki Pool as an immediate action to cause maximum damage.
GP