Color solve this one problem just like they solve the text equivalent better than annotations. This is not fundamental.
> lacks good mechanisms for abstraction, reuse and hierarchical structure
VLSI circuit designers have some abstraction mechanisms that are not that bad. This one is fundamental, but it's not as bad as most people say.
> It doesn't have tooling for refactoring and typically lacks tooling for performance profiling.
I can't imagine how those could be fundamental problems either.
In principle the largest problems of visual programming are our lack of capacity of understand complex images, compared to text, and the added information that most visual languages add (making the complexity worse) (that do not apply to things like GUI designing). I don't see any other showstopper, but those two are really bad.