Japanese warships must be judged against Japanese doctrine

Were Imperial Japanese Navy ships fundamentally flawed compared with other major navies?

No; they reflected Japanese Pacific doctrine, and defeat does not by itself prove bad design.

Japan's defeat does not by itself prove that its warships were badly designed. The ships served the Imperial Japanese Navy's own concept of fighting in the Pacific rather than American or British requirements. American material superiority and good fortune mattered greatly to the outcome, while Japanese command arrangements also deteriorated under wartime pressure. A warship should be judged against the doctrine and conditions it was designed to serve.