BOTW is amazing, but if is has one huge flaw, it would be the notion controls. I've had to use cheese strats on almost every motion control "puzzle" (not really a puzzle when you solve it and are relying on getting lucky) because most of them are absurdly hard. Take the maze puzzle, for instance. I absolutely could not beat it without using stasis to cheese it. I spent an hour on one puzzle, purely due to horrible motion controls.
Ending this off on a positive note, that is really the only major flaw I can think of, with only minor flaws otherwise (such as durability).