Putting a more powerful engine in a Zero would not have done it any good. Above 275 MPH it was pretty much impossible to turn, no self sealing fuel tanks and one piece of armor in the back of the seat made this an obsolete fighter that would have been better relegated to training or non-combat duties by 1942. Addition of all of the necessary stuff would have changed weight, CG and a number of other things that would have had to be engineered for. Better to spend the time designing a new airplane.
True. They did design new aircraft to replace it - Ki-84 etc - but most were land based planes and not carrier capable (correct me if I am wrong).