IF by 'JKD' you mean the techniques that Bruce Lee used (a la 'Jun Fan Gung Fu'), then I would say there is quite a lot of focus on parrying and trapping which may not work in a real-life situation, so I think the biggest threat to that kind of JKD is an opponent who is quick to shoot in and takedown and is good on the ground. BL's arsenal was notedly lacking in ground stuff
AFAIK.
BUT If you take my personal interpration of what JKD means to me, I guess the biggest threat to it would be if the opposite was proven.
So if my definition of JKD is "a collection of techniques that works best for me", the biggest 'threat' to that would be someone coming along and saying:
"NO! I have proven that it's 'better' to adopt techniques that DO NOT work for you!"
or
"NO! I have proven that all you need is technique ABC, and NOTHING else!"
and many variations and degrees of the above.
So you see how your question does not really make all that much sense from my perspective?