I was thinking maybe you cud add theese into the game to make it more realistic :

1. Genjutsu/Nin resistance : thats just to say how long a typical genjutsu would last on you or how much damage the ninjutsu would take. Genjutsu resistance can also take a part in the jutsu "Kai (cancel)" If your gen resistance is high enough to fight of a genjutsu used on you then you would have a higher chance of actually cancelling the genjtusu of a stronger oponent.

2. Making different clan training grounds : That is to say that each clan has its own area in which to train in a village . A village such as the leaf would have a more diverse set of training grounds because of its many clans. But this can help the young acedemy students and genin to learn from higher ranked people in their clan without the distraction of being attack from some other clan in the process of learning. These places can be a safe haven for the different clans to communicate with each other and the elders can teach the younger onees new jutsu and tactics for using their jutsu in the right ways.

3. Making a system for jutsu clashes such as a water dragon missle(suryuudan no jutsu ) or a fire dragon (ryuuka no jutsu) clashing the outcome can come in two different ways :
A. If either ninja's ninjutsu is of a higher level then one jutsu will overpower the other leading into a full on frontal attack giving double damage to the perosn hit.

B. If the ninjutsu of the two ninja are basically equal then both jutsu will cancel out with an explosion of some sort throwing the two ninja back causin minor damage to both.

4. Making a medical ninja training school : If this is implemented medic ninja cannot be chosen as clan/race at start but will have to be earned by going through a training session in school much like a academy student becoming a genin and so on. But the catch is not everyone can become a medic ninja there is a certain percentage at start that u will be have potential in becoming a medical ninja (as you will have to check with Tsunade or some other medic teacher to find this out) after becoming a genin. Much like being born with the potential of cursed seal or kyuubi in other naruto games.
The course of training to become a medical ninja will most likely take place in three steps.
A. A mission to find a medicinal herb that can only be found in a certain part of the map along with other items to make a proper healing potion or whatever you wanna do.
B. Having enough chakra and chakra control to revive and unconscious animal (small fish o puppy or something) . This can work by draining your chakra to put into the animal to revive it along with your chakra control controlling how much chakra is used in each insertion of your own chakra.
C.Other stats appear under the stats tab after finishing step B this is your last training. Also a medical verb appears in commands somewhere or in ianother tab of your choice. In the stats it will say Precision percentage much like seal accuracy or so and the verb you will get is focus chakra precision. This is used for putting the right amount of chakra into your hand for cutting tendons or paralysis. After this training is done you are now a qualified medic.