Make the characters a little more different
Some characters should have stronger melee and weaker melee-example tsuande should hit harder then shikamaru.
Some should be faster then most- haku or lee for instance, while some are slower like garaa(which also makes me want to say characters like garaa should have higher defense than most)
Some should have more health- first hokage, naruto-since they are senju
Some should have more chakra-like hyugas, and senju.
get rid of those damn sleep and stun tags.(completely killed custom ranked)
More combo and jutsu variation. Perhaps custom jutsu per character.
Interactive environments, destructible environments.
jutsu clashes
Better team ultimates. And more benefits to people who use ACTUAL teams. (itachi kisame)