That is sort of the point. I mean effort/cost-wise we should admit that the Kami armor is WAY more expensive then the Runic, heck I think it might even be higher then a full suit of MPS armor (haven't messed with that mod much). It should be better. That's the point of the cost in effort and materials. You basically need to be able to farm the Wither to make it.
The Thaumic Tinker's enchants on Thaumium armor being so much better then the Runic set is a bit of a problem, but on that could be solved by a few small buffs to the Runic set on the utility side. That seems to be it's main weakness, that it doesn't match in movement or effect (drowning, falling, underwater slowing, etc) protection, not the keeping you alive part.
Then I think all the magic armor options would be near where they should be in terms of quality vs. cost. But that's just my view of it.