Ok before I start I wanna give credit to Albedo for getting me started on this, he did just as much of the thinking with this as I did.
You no longer choose a new specialty when you start or after a Oro kill.
Instead there will be a new place added in the Academy where you can go and learn Jutsus from different Sensei.
These jutsus will cost you to learn, each will have a Gold and Gem cost.
Also each will have a 'Jutsu point' cost, jutsu points will be found by adding Intelligence and Oro kills together, or something like that.
This limits the amount of jutsus you can learn at any point, so a rich Acad or sitter couldn't learn all jutsus.
Once you learn a jutsu it will stay with you forever, over Oro kills etc, only way to lose it is to reset.
Also the jutsus would be broken into Ranks, Such as B,A and S etc... which would provide Oro kills limits, so to learn S rank Jutsus you would need to be at 50 kills or higher.
Now this system help the Specialty system become more like that of the series, in which you go and learn jutsus from your sensei, and you can create kewl combos.
Also since the amount and strengths of the jutsus Depend on Intelligence and DK, it also makes it more like the series, that way if you focus on increasing your Strength and Defence, you wouldn't be as good at Ninjutsu, much like Lee in the series, and the other way round is true, so if you focus Ninjutsu, you physical strength will not be as strong.
So this brings more balance to the game as well.
This could be extended to make Jutsus appear randomly each day like mounts, so not only would strong jutsus be expensive, but rare as well.