It's easier to design for scale-out than one might think; a great resource to get started is http://highscalability.com.
Regarding EBS, I haven't seen the hangup issue you've described. Any data?
As for low inter-node latencies, Amazon has an offering that specifically addresses that need: http://aws.amazon.com/ec2/hpc-applications/
Overall, I think Amazon is making a lot of inroads in areas with specific hardware demands. They just launched GPU compute options, and I expect we'll even see SSDs soon.