So I guess it's my turn to contribute with something. 

I've been in many Naruto-games over the years, and started playing in the world almost as soon as I had watched the first episodes. Those I received on three CDs, each containing four episodes, so I've been doing this since episode 12. One of my all time favourite games was actually split in two, a concept I would very much like to try again if I just can get the right group for it..
Everyone played a ninja from Konoha and almost everyone had to start out as a genin and part of a team. The jounin were hand-picked by the GM and missions were abundant. After only a month or so the first chuunin-exam was held and some made it through, which opened up new genin-spots to fill. This was roughly at the same time as the great filler season was going on, so the whole game had that early-series feel to it. 

The second part meant that everyone also had a second character. A member of the AU-akatsuki. Remember that this was before the real master plan was revealed, so we weren't really sure what to do. Their main goal was to capture the bijuu, but to become the jinchuuriki themselves and use their powers to eradicate the village-system and bring about an age of chaos which would lead to an era of strength and stability. Of course, this meant that every now and then the two worlds would collide. The tiny genin you had spent weeks molding into a perfect miniature-badass now stood in front of a super-dangerous S-rank criminal. Both of them characters under your control. 

Logically the genin should die in every encounter, but anime logic is different. Each player therefore had to give it their all to both make their akatsuki member as badass as possible, but at the same time allow the genin to escape somehow. Sometimes they did die, which meant that the team was now one man short and the guy they had trained and fought with was gone. Near the end of the game one team nearly went full Shikamaru and started to hunt down the akatsuki. As a player of the team they were aiming at first I would have had so much fun pimp-slapping them all the way back to mummy.