Why not set meditation as the player-character's 'last resort', so to speak -- in that it would regenerate chakra/stamina, but at an immensely slow rate (perhaps stamina would recharge faster by ratio comparison, though only in this state); And due to the nature of the act, it could also slow (not halt) the process of stacking poisons, et cetera.
Food&Drink would then dramatically increase chakra-regeneration/stamina (with chakra-regen being the higher ratio here, as a counterpoint to the meditative-state) --depending on the food, and thereby creating a need for chefs-- but at the cost of exposing one's self for a few seconds via a required consumption animation; Pills, on the other hand, wouldn't be have an varieties capable of increasing chakra-regen/stamina, but could be consumed on the go.
And perhaps, as in Oblivion, rest could be used as a gateway for access to the character's next 'level', if you will. I.E. The character has just trained to the point of easier manipulation of a jutsu, but they must first rest before it's fully unlocked for them; Alternatively, rest could just be used as a means of getting the most out of your character's performance -- maybe a rested character gets an additional buff that decreases stamina and chakra consumption after performing tasks, at least for a decent amount of time (10-20 minutes?).
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