Google had build a highly customized, scaling environment based on their own software layer instead of mere "linux boxes". And clearly it worked great for them. So that's basically what they offered with GAE.
But the problem in the market was that GAE was this weird custom thing, while Amazon was selling a "cloudy" version of the same environment all the developers were already using. So Amazon won -- the market wants linux boxes, even if they aren't as scalable or efficient uses of hardware as Google's stuff.
The point is: Amazon won by circumstance. They happened to have an internal product already that they could sell, and they did. Google had an internal product too, but for reasons beyond the control of its designers, it wasn't a good fit for the market. I don't think either of these has anything to do with being "great at doing business".