For chakra system i say like this : its a pretty big pool but regenerates hard and there wont be chackra pots at all only chackra transfer from player to another or jutsus that absorb chackra,there could be like conserving chakra mode that works like this : if you dont use any chackra consuming things like water walk ,jutsus etc you go into a state of faster chakra regeneration,however any chakra related actions will cancel the effect for x seconds

.and with the clans im thinking like the clan that is similar to senju could have increased stamina(health and can run more without tiring),a bigger chakra pool and if the system is that some lucky players get kekkei genkai the first "senju" chosen to have the things above can use wood style but that cant be passed since only hashirama used wood style.

,for uzumaki like clan just a slightly bigger pool than "senju" and are good with sealing tehniques

And the health should be very high,like when you start you have 700 health and A rank jutsu do like 500-800 damage so that you dont die immediatly in battle after and for the death penalty i think perma death is to cruel:what about losing all you got on you but if you learned an ability(assuming you have to click something to learn not just know the handseal) you keep the ability to do it but you lose the scroll with how to do the jutsu and you keep your stats
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