"What are you eating?"
Co jesz? or "Co ty jesz?" is ok. ( Although using ty jesz is a bit awkward in speaking )
czego nie jesz is what do you not eat so why not czego jesz for what are you eating
"jaki" generally is more in the direction of "what kind", like "What kind of bread are you eating?" - "Jaki chleb jesz"?
I get what you're saying, but you can ask other "Jaki jest" questions, right? Like "Jaki jest twój ulobiony kolor?"
Yes. So far I think the "Co" vs "Jaki" is absolutely the hardest question for me to answer, I have no idea how to approach that distinction. Of course it's obvious to me, but how to explain it...