Don't include Naruto. Please.

I like your idea to include Gai and Kakashi, and also Lobster Magnet's idea to flesh out the Leaf Jounin. Definitely more focus on them, rather than the Rookie-Nine. Personally I'd prefer the idea of focussing on one or two teams and their respective missions than a larger story, but do include lots of big military fights and wars and shit - that is if you want.

I'll try and think of some good Rock nins if you need ideas too.