Yes. That's it. Only, it's not a specific "flaw", but a combination of all the weakness, and subtle implementation issues that every system has, which add up to "colouring" the overall sound, and "liquidising" the critical low level detail.Suppose 99% of audio systems had a flaw that meant that even though they might be very expensive and measured flawlessly in all conventional measurements, they were subtly blurring together the musical ingredients into a 'soup'. Individual ingredients no longer had their own satisfying textures and flavours that contrasted exquisitely against others because the system was liquidising them all together at some level. The only thing you could do would be to season the soup to the best average taste you could - hence tone controls, EQ and the use of 'room correction' ("It's definitely not a tone control, honest").
Perhaps there is such a flaw, and people can't imagine how it could be any different.
http://www.linkwitzlab.com/Attributes_Of_Linear_Phase_Loudspeakers.pdf
The alternative - when the system maintains the true separation of the ingredients - would be that you wouldn't even think about tone controls because each individual sound was fully-formed and self-contained.
The good news is that there seems to be almost no limit to how far one can go to "clean up the act" - I certainly haven't found such, so far ...