The thing is, the "God moves in mysterious ways" is a completely valid response.

Think of it differently, think of it God was an alien (more likely IMO). NDT has a pretty good bit on this. If we are 1% smarter than apes, and we can understand so much more than them, then a being 1% smarter than us must be able to comprehend things we can't even begin to imagine. Think of a being that is to us as we are too ants. There is no way we can explain calculus to an ant, in the same way there must be things that being understands that it can in no way explain to us (and included in that may be, why bad things happen to good people).

Or look at it from a Chaos theory perspective. A butterfly flaps it's wings and all that. Maybe those eye eating bugs are some how a necessary byproduct of a minor event millions of years early which if it didn't happen wouldn't lead to eye eating buts but would lead to Hitler winning WWII.

Or much more likely. God (if there is a god) created the rules to evolution (which is what people who believe in both god and science believe) and those rules necessarily lead to eye eating bugs. A change in those rules could prevent eye eating bugs, but would have also prevent humans from existing.

Of course, this does depend on what you mean by omnipotent. Does omnipotent mean you can do anything, or does it mean you can do anything that is logically possible. Could god make 2 + 2 = 5? If so, then yes, there is no reason for bad things to happen to go people. But if you think that 2 + 2 can never equal 5, but that God exist, then you have to believe that god isn't so much an omnipotent being as he is a sufficiently advanced entity such that his technology appears as magic to us.

Now, I'm not saying that is a reason to believe in god, but just it depends on what type of god you believe in (the Clockmaker god, logic defying god, alien god, etc).

My response, if god existed, would be just be "Why?" or "Which type of god are you?"