Ok God! What the hell is with small children and cancer?
“What is the point of you?”
Why did you make suffering?
Loan me $50?
As a lifelong atheist I wasn’t serious about a question I’d want to ask. I was, however, trying to be funny about the point of asking an omniscient God any question at all 
I can’t improve on this, wish I’d thought of it.
Why do good things happen to bad people?
Where is the +1 button?
Why do bad things happen to good people?
Why have you stayed hidden for so long?
Seriously, God, I want to know where I left my keys.
I would ask him “Why quantum mechanics?”, and “Why turbulence?”. And I am fairly confident I would get an answer to the first question.
(Attributed to a variety of physicists including Heisenberg, but with the way misattributions happen, it was probably a less-famous one).
Why are you so inordinately fond of beetles?
I wouldn’t have to ask him which afterlife Nee-Nee and Pop-Pop are in; if Heaven exists, they’re there, no question about it.
I’d want to know where Grandpa is after a lifetime of treating me and Mom like the scum on the bottom of his boot.
Was I a Nazi or other evil person in a former life?
I want this answered for reasons.
And, where is @panache45 s lost red sheet. This seriously bugs me. 
…
Can you go back to the drawing board and re-design the spiders? 4 legs and bunny heads would be good.
I was going to post, “Why does a God that is all-knowing and all-powerful need to be worshiped?”. But I like your question better.
As someone who does worship God I don’t ever recall being told God wants worship. It’s a way to honor God, not fulfill a requirement.
I suppose “how’s it hangin’?” would probably be a bad idea.
Sure, there is no difference in your chances of going to heaven based on whether or not you worship god, but be sure not to worship any other gods, there’s a very clear commandment about that.
When you go to church and worship God, how do you know whether you’re worshiping the God of the Bible, or some “other god”?
Is the penalty for stealing or adultery the same as worshiping another God? All three are forbidden in the same place. Suppose I don’t honor my father because he beat my mother and abandoned us when I was two?
" And what if we picked the wrong religion? Every week we’re just making God madder and madder. " - Homer Simpson