I am going to take this somewhat seriously because I have high hopes for the game! Obviously I don't know if all of this is possible, they are just ideas. Also I am unsure if I am doing this right, so I apologize ahead of time.
Custom Jutsu
Using a spell system in order to create Jutsu using different attributes and variables. For example, using the 5 elements as "variables" while using other effects such as a projectile that comes in different sizes (a Giant Fire ball, or Multiple Flying Rock Jutsu), or a wall of water or wind that moves forward or is defensive in nature, something summoned from the ground (ex. flame vortex on specific spot that's pointed to by player within range). From there you could add even more effects, attributes or variables (whatever you wanna call it) such as power, speed, flexibility, fire-rate, range, spread, AOE etc. Maybe creating elemental weaknesses/strengths that debuff or minimize offensive damage.
Squad System for Kage or Jonin etc.
It would be interesting if the Kage could form teams/squads based off who is in need of one (ex. Genin puts in app for squad > gets put in with 2 others & Jonin/Chunin etc.). Also thinking about activity from the player, character level, playstyle etc. in order to form said team. These teams can be given missions as a squad, that can be completed when everyone is online. Said teams would have specialty's like tracking, elimination, or scouting or be an all-around squad. Teams could have a leaderboard/renown for each village. I understand this is somewhat already implemented but my idea retains around having the Kage or a high ranking member of the village look over applications that are put in through the game after certain conditions are met.
Again, I do not know if I'm doing this right or not. These are just ideas, please do not get offended.