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I'm sorry to hear about your kid's suffering. My son was born with a heart defect and required open-heart surgery when he was 3. It's so hard. He has since had other heart complications, including seizures and recently a stroke. I'm sorry for your pain.

So why does God allow it? There's a long explanation to this, but actually if God stopped all suffering, we would stop being human. We'd be robotic, with every action and thought governed for us to prevent any kind of harm. God would have to eventually regulate all of our actions and even all of our thoughts if pain were going to be removed from the earth. Instead, He most often allows life to take its course. He created cause and effect to work. If He intervened regularly enough, there would be no such thing a science (cause and effect would be too unpredictable), reasoning (things wouldn't make much sense), and even things like love (God would have made us do it). God doesn't stop the pain. But then we see many ways he redeems the pain: courage, strength, stamina, fortitude, people who come along side of us in love, and a hundred other things. While you'd prefer to have your child in good health than fortitude because he/she doesn't, God promises to make good on the pain in our relationship with him. If he stops the causes of all pain we become less human; if he strengthens us through and after the pain, we become more human. While the suffering of our children is awful beyond compare, it doesn't make God unloving and uncompassionate to allow it to happen. Just as a surgeon or an oncologist allows suffering for a greater good, so also God can allow suffering as long as the balance of good over evil is sustained, and that good can come out of any suffering. And while that doesn't make your pain any easier, and I'm so sorry for your pain, the existence of suffering doesn't mean God kind of a jerk.

The real answer to this is so much longer, but I don't want to just write a wall of text while you are aching in your heart.

I recently had my first child and we were emergency transferred to a children's hospital. There are breathing issues as well as some neurological stuff.

My question is this: if God is supposedly all loving, then why do things like this happen? What possible plan could God have for this?
The neurological stuff could result in seizures, which could be surprise baby death. We can't treat them pre existing so it's kind of a gamble with our baby's life. Things are looking ok now but the neurological issues are definitley there. I've heard all the typical responses - god is teaching you to lean on him - in which case - he's kind of a jerk that would cause a lifelong issue for a baby to essentially force me back to him. If that was the case why would I want to hang out with him anyways? Sorry for the rant but I'm wondering how those of you out there have reconciled child suffering with an ultimate plan?