Maybe some clan traits would be good? I'd like to hear other peoples ideas on this as to what they should be. Here's what i came up with off the top of my head.
Uchiha: Increased starting Genjutsu, Higher Genjutsu gain rate.
Nara: Increased starting Chakra, Jutsu use 5-10% less chakra.
Kaguya: Inherent def boost, Higher def gain rate, Small boost to starting hp.
Puppeteer: Increased damage when using weapons, Increased Ryo gain.
Idk anything else right now but like i said, ideas are very welcome.