Our senses are based on receiving stimulus from the environment. Our environment is a reality, built using light as a building block. The different shades of colored light indicate how the vibrations of the environment are outgoing/incoming to the person and environment.
Personally, I feel there is little rigor in the chakra systems. My belief is the ability to visualize is underdeveloped which makes real empiricism difficult. The amount of practice it takes to 'really' use an energy system is underestimated by most.
Meridian theory is interesting. The earth is the centralizing grounding force where the sun/cosmic is the rising outward force. The idea that balances/imbalances express themselves thru a complex of points along lines of forces where ethereal energy runs is the most sophisticated and powerful in application in my view.
The general difficulty of reliable application is the way the system's correspondences are understood. Most use very subjective ways of probing a balance. The visual aspect of the chakra system works nicely with the proprioceptive nature of meridian theory.
Besides the 'objective' methodology of using a energetic model when attempting to heal or develop, our society has a predisposition to see things in overly rigid terms where there is a definite process where a result must be achieved. So the general bias is along the lines of "how can I achieve this result" rather than "how did this result occur". In most healing processes the natural process of balancing is interrupted. The resolution is seen as being 'fixed/cured' rather than realization existing perfection.
The main purpose of a system is consistency. So primitive caused so many different ways to understand the same thing that there is no understanding.