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Damage a pokemon takes is split into "lethal" and "non-lethal". Or critical, or severe, or whatever adjective you think works
The details of what determines it can be fleshed out later, as well as a more friendly name, but basically, part of the damage a pokemon takes is permanent for the battle and can't be recovered past, except maybe by a specific berry or signature move.
Some moves would be fine tuned to deal more or less than others, some moves would specifically target that buffer of recoverable HP, various items could boost or lower a pokemon's lethal damage output, and so on.
Say, just for example, Pokemon A uses Flamethrower on Pokemon B.
Pokemon B takes 100 points of damage, with, say, 30% of it being lethal. It only looses 70 of its basic HP, with that last 30% coming out of the recoverable HP, being "lethal" damage.
Maybe if its a crit, the 1.5X damage boost is only the non-lethal damage, while the lethal damage gets its own independent 2X multiplier or something.
Not only does this hamper long-term stall, but it also hinders hyper offense, since it's now much harder to OHKO a pokemon now that 30% or so of their damage is being shaved off, bringing things to balance.
