In my opinion the only major weakness (karate-wise) of Shotokan in Japan, is the adherence to often outdated, and more importantly, non-karate-specific junbi-undo (preparatory exercises). More than adhering to tradition, this is the ‘cultural result’, of lacking the ability to understand individuality; that is, that all human beings are different… Every individual needs to approach stretching differently in accordance to their own physical attributes/genetics, deficiencies, age, injuries and the highly diverse combination of these variables.
My point here is that we do not do karate for the warm up or stretching. We do it for karate. Therefore, as long as we can optimize our karate technique and skills, the warm up/stretching we use is irrelevant. Optimal preparatory exercises are twofold… The safest method (to avoid injuries), and the best means to maximize our execution of karate itself.