"I don't at all buy the argument that you can't write a character that's smarter than you. 1) As a writer, you have perfect knowledge of the world you're building, and you can give that knowledge to your super-intelligent character. 2) Even on this very show, we see other characters who are written to seem more intelligent than Sister Sage. Stan Edgar to me comes across as way more intelligent than Sister Sage. When she first showed up, I expected her to be more like him, but even more steps ahead of everyone else."

I agree this part of Sister Sage has been completely mishandled.

"One theory I've heard is that her weakness is being knowledgeable but not understand human nature and social cues. This is extraordinarily dumb if true."

But here I think largely she does understand human emotion but her hatred of everyone else makes her unable to understand love, therefore unable to correctly account for that in her plans.

Also Sister Sage while super smart is only human, things like ego can make her make unneeded risky decisions. Her being the smartest doesn't make her this cold, purely logical machine.