
Dasrak |

I have no idea what the authors of the Chakra system were thinking. It's completely unusable in its presented state. It drains ki quickly, you risk damaging and/or incapacitating yourself if you fail the saves, it takes several rounds of continued use before the decent abilities are available, and to add insult to injury it consumes your swift action economy.
Most of the chakras are pretty tame, too. The damage reduction of Root is outweighed by the risk of damaging or dazing yourself, Sacral is a joke (you know what I call "flight" that begins an ends on a solid surface? Jumping!), while Navel and Heart don't scale with character level and are completely useless by the time you're high-enough level to use them. It's only once you hit Throat and above that you start getting decent effects.
Serpent-Fire Adept is a thing, and is probably the only remotely usable way of using this subsystem.

Dragonchess Player |

As written, the chakra system is not good at all.
Some homebrew modifications here and here help a bit. Overall, though, the qinggong monk or esoteric magus (with one adjustment) are probably a better routes for a "chakra adept" than the chakra system itself.