I have a couple of suggestions i'd like to post here, so please take some of these into consideration .
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I've taken some of the ideas from the Naruto based Roblox game, 'Naruto Shippuden Online Adventure' (I'm trying to keep this ad-free so i won't post links)
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-Choosing Jutsus-
I'm not sure about how this system will work but i think this is how it should be done:

1. There must be an icon/button you click to choose your jutsus.
2. After choosing the jutsus, you will have an option to bend the chosen jutsus to the key-board keys you prefer.
Then later on, you can use the keys to perform jutsus (BUT, you cannot perform the same Jutsu twice in a row, example: Have a small amount of time between performing the same Jutsus 5 seconds as an example, or more time depending on the type of Jutsu).
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-Chakra-
I have no idea how this will work but as a suggestion:

1. There must be a Chakra bar somewhere showing on your screen.
2. A key must be pressed to "re-charge" your Chakra.
3. Everytime you use a Jutsu (or something that involves using Chakra), your Chakra decreases (also, the amount of chakra decreasing must depend on which Jutsu/Technique you used)
4. Your Chakra amount grows up (your Chakra bar also extends) as you "level up".
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-Taijutsu-

Performing this should be more of a Hack 'n' Slash/Slice 'n' Dice type.
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That's as far as i think for now, but i might be adding more suggestions.