Chakra Reserve: Remove the current system. You gain 1 point of Reserve plus CON modifier plus 1 per 5 levels(a 20th level character with CON 20 has 10). As a standard action you may spend a point of reserve to regain 1/4th of your total chakra points, or 1/4th of your total hit points. Whenever you are reduced to 0 HP, you automatically spend 2 points of Chakra Reserve to regain 1/2 your total hit points. When you are reduced to 0 HP in this manner, the extra damage from the attack is negated(You're at 40/100 HP, you get attacked for 50 damage. You go to 0/100, regain 50 hp, and the 10 damage left over is discarded). This change is mostly to make combat slightly more cinematic and allow players to make mistakes without rocket tag coming into play.
Skill points: 2 extra skill points per class, spent freely.
Techniques Known: 1d4+Level always annoyed me, so I was thinking about giving them away based on your highest mental stat and appropriate ninja rank. Genin are *1, Chuunin are *2 and Jounin are *3(Younin would be *4 and Kage *5 if you want to extrapolate past Jounin). So a genin with Intelligence 16 at chargen would have 16 techniques, while a chuunin would have 32 and a jounin would have 48. Further, all characters know all E-Rank techniques that they could normally learn.
Technique Rank: You may only have a number of techniques at the highest possible rank equal to 1/4th your level(rounded down). E.G: At level 12 you may only have 4 rank 12 techniques.
Masteries: Mastery levels are bought as if they were techniques.
Feats: Genin/Chuunin/Jounin are given away at levels 2/7/12 automatically. All bloodline feats give a bonus feat when taken, this bonus feat may be any other feat you are eligible for(essentially removing the feat tax from bloodlines).