(Please let me play the theist role for this one, this should be interesting indeed)

God's PLAN is always PERFECT!
God does heal amputee by inspiring people to create fake limb.
When god does not heal smallpox back then, it's because god PLANS to punish human, and then forgive them afterward.
Just like when u punish your kid, no dinner tonight, but tomorrow u forgive him/her and give special treat. (Pizza maybe)
When bad things happened to good people. It's because god's plan to teach them a valuable lesson.
When they're dead, god take them to better place. god actually saving them not to suffer in this world anymore.
Or maybe god need them as an angel.
It's called plan. You atheist are pathetic. You don't understand god at all!