Could this be phrased with a different word order?
As in could you say "Ni parolas pri kio?" and still have it mean the same thing?
It seems that questions in Esperanto start with the question correlative. "We are talking about what?" is a little odd in English, and this seems to also be the case in Esperanto. Perhaps Yoda phrases his questions like that, but I am uncertain.
What about "Kio ni parolas pri"?
No, that's not correct. It has to be pri kio as in the example provided by Duolingo.
why isnt "kio" in the accusative case here?
Because of the preposition - the answer also won't have an accusative marker because it will be followed by pri - Ni parolas pri la vetero. We are talking about the weather.
Shouldn't "diras" be more accurate?
According to tujavortaro.net, diras is like "telling" or "stating" and parolas is like actual verbal speech.