I’m not sure I’d bother with “Why?” After all, if I’m in front of God, I can probably figure that part out.
I’d be much more interested in the “How?” part.
Of course he/she can - he/she simply starts with extremely large values of 2.
And extremely small values of 5, of course.
Is there any reason you’ve come off as such an unremitting asshole for so long?
I feel safe in asking that one because, if God exists and is offended by such a question, I’m going to hell anyway.
Given the fact that you made man in your own image, and you gave Mankind your only son (It would would be rude to ask God why a workshy scummer can have half a dozen kids while he can only manage one…)
Why did you make the The Universe so big?
What’s the purpose/meaning of everything?
"So you have the power to do anything you want, absolutely anything at all, and you’ve created a world (maybe worlds) with unimaginable levels of suffering.
What the fuck is wrong with you?!"
I’d want a story. Just gotta figure out the question which gives an answer worthy of 100 generations of family history.
What makes you laugh?
This was my first thought. Or Why Me
An honest question: “Is it true that you really love me?”
My cat died. He was awesome. Is he up here too, or is this place only reserved for humans?
What’s the point of me?
Do you think Bender did a good job at being God?
What are your secrets?
Or alternatively:
Given that You are omniscient, You already know the question I’m about to ask. What is the answer?
To which God replies:
“Yes, I do send people to hell for trying to outwit me and other forms of smartassery, and yes, you are going to hell for that reason. Right now in fact.” 
How can I continue to exist beyond physical death?
Which was your favorite NFL team before the Dallas Cowboys?
Shamelessly stolen from Suttrey(sp?)
Why did you have me in that crap shoot down there? I could never put two parts of it together.