Even though he is "all powerful" and could stop this he chooses not to, Surely by any ones defenition that is cruel."
So God should make everything really simple for us? No trials, no afflictions? What would we learn from that? And before you say what can you learn from afflication, the answer is a lot. You can come closer to someone in affliction, then any other way. It makes you humble, it makes you remember that you need other people, etc. And if you succeed over your afflictions, you come to appreciate life. Ask any cancer survivor, or car accident survivor of their experience, and they will tell you how much they appreciate what many take for granted. It is a time for personal growth, and inner reflection. As far as those who die from these events, it was their time to go. Death - to the believer is not as terrible as it seems. Everyone will experience it. Everyone will witness it. If you believe in an afterlife in any form, then it is a release from our temporary state, into a limitless existence.
"he waited many generations before he sent help" - the atonement is believed to be everlasting. Covers all time before and after, therefore he could have come at anytime.
"Tree of Knowledge of Good and Eveil" - and what was this tree? to know pleasure and pain, vice and virtue, etc. They partook of the fruit, to know the difference between good and evil. That's not cruel. You can't know good until you know bad. If everything was good, then good wouldn't exist. It needs its opposite. If not, they would have forever stayed in the same state. Never changing.