My suggestions based on seeing certain things. I am not sure if some things have been confirmed already, so I apologize for anything that contradicts the stuff.
If the affinity is random, I would suggest increasing the chances of getting a certain affinity based upon the village you live. For example, if you live in Kirigakure or Amegakure you have a greater chance of gaining water affinity. This would also extend over to each clan, based upon the affinity tending to be with the certain kekkei Genkai.
In times of war, the road to becoming a chunin should differ. When the village’s ranks are low, I think that village should be able to promote more chunin. This could happen too when the village is not in war, and they need ranks to be filled. Going back to the war bit, we should be able to have alternate methods of becoming a chunin, aside from the exam. For example, because of war, the Genin forced to take a high ranked mission, alongside his team, has a promotion chance via the success of the mission (Think of Kannabi Bridge). I believe this will help the ratio of ninjas per village. Maybe, doing these missions has a double experience bonus, unlike regular Genin missions.
Mentioning a council, I agree with positions. Just like an actual government, the face of a nation is by its politics. It would be nice to see a village impacted by these politics, and divided by them too. For example, one nation could be more radical or conservative. During Kage Meetings, it would be nice to see the confliction of politics. In addition, a Kage election should show the impact of these politics. A Kage who does not mirror the beliefs of a nation should have a hard time in the election.
Every Kage should have spies. These moles bring back a report: increases of village guard, how many Genin promoted, positions of ninjas (only the occupying areas), and the candidates of the upcoming Kage or council member election. These spies are NPC’s, or automated letter. Only thing they cannot track are Anbu/ Hunter Ninja movement, etc. As the masters of concealment, Anbu, who passed through the ranks, are able to gain the duty of protecting the Kage, Patrol, Information gathering, and Assassination. Their actions influence how much information the spies gain.
During Chunin exams, it is the Kage’s choice or Defense Director with how ninjas are set up to guard the village. I think it would be awesome if the Kage has the option to look at a map or crystal ball, showing the entire village, and be able to emplace certain Anbu units and other ninjas. When a Kage wants to invade another village, it would be cool if they can organize the points of attack or other plans.
Gate Duty is something I would love to see. My suggestion is to use it similar to jury duty. As long as you are chunin and above, you have the chance of random selection for this duty or you have the option to enlist for a certain time. I think everyone should have to guard the gate occasionally.
Next on the list are pvp suggestions. I would love to have warzones, open world pvp, and village invasions. The last one would be hard, because of balancing, but I think it would be worth it. Tying this to Bijuu, I would say only nations with the lowest population should have them, or more of them. Like an Ace in the deck, this will be able to balance the fighting power of nations. If we cannot have these invasions, I would like to see Kage duels. In the Chunin stadium, we see the two representations of the village duking it out. Behind a shield, (think Sarutobi vs. Orochimaru) no one is able to interfere. Whoever wins, deals a major blow to the other nation. However, not all is lost. The now losing, crippled nation should be able to have a chance to come back. In warzones, open world pvp, the meter between winning and losing the war should be shifting. I do not know how such a meter would work, but I would prefer it to war weekends.
Mentioning teams, I would like an option to form a team manually or join a queue. This way you can invite your friends when they are on, and then you can join a queue when they are not. If enough people are not online or population is too low, NPC’s should be optional. These characters mirror the difficulty of the upcoming mission or assignment.
Acquiring a Bijuu or sealing them just seems like a problem waiting to happen. In my opinion, I would prefer not to have the ability to capture it because you are strong enough. In Naruto, fate has a way of picking certain people. I would like it, if when the village acquires one, a new ninja, or an old ninja randomly picked to be it. Now, if you beat or seal a Bijuu, you should get some kind of reward. Maybe, the character will gain a special title like Sannin. Once again I wish the amount of Bijuu, reflect nation’s population. If things are even populace wise, there should not be as many. When a nation is low, they should have a Bijuu or jinchuuriki. Heck, I would not mind if the sealers only partially impress it in a certain ninja, which allows the Jinchuuriki to change hands based upon changing population.