Hey. Just a few combat ideas:

Ninjutsu:

On Hand Seals.
 
A character to have an inbound chakra nature.
Also, if it could be worked so that the character could learn "change of form" and "change of nature", as Naruto did learning the Rasen Shuriken, that would be excellent.
I don't know how practical it is, but hypothetically it would be amazing. You could perfect different changes of chakra form and different changes of nature.
Imagine a Chidori Rasengan, or a Multi-Shadow Clone Phoenix Flower?
Then, I suppose we'd have to think about chakra levels: would it work like mana does in most RPGs, where it would deplete and then refill?
Built-in chakra nature advantages, i.e., fire defeats and becomes stronger against wind-style, is defeated and nullified by water-style, etc.
Also, offensive/defensive hand seals.

Genjutsu:

The ability to "lay" a genjutsu, as in how you can "plant" a "rune"-style spell in Skyrim, for example. The genjutsu would trigger when someone walks into the area.

Taijutsu:

A system activated upon proximity, similar to how hand-to-hand automatically activates in "The Bourne Conspiracy" game?

Offensive factors: Speed, variety of techniques, stance/style switching, etc.
Defensive factors: HP, Parry/block/dodge system, counter-attacking, combination fighting.

Perhaps a choice of kekkai genkai suitged to the game, where one of the three would be enhanced at the cost of the other two, as well as an "all-rounder" option where all three remain initially balanced.

Just a few thoughts, guys, thanks for reading