Isn't this "flaw" a balance of features vs reliability? In most cases it's ok that the API spans the entire region, and makes it easy to address one API endpoint per region, allows Amazon to offer everyone different availibility zones within the region, etc.
The issue being that availability zones don't get throttled when they start to overload the API. The control system should have automatically throttled the misbehaving AV.
Which is probably far more difficult to do properly than I can imagine.