In case you are connecting to various EC2 instances frequently for testing purposes, the following SSH config might be useful for you:
host *.amazonaws.com
User root
StrictHostKeyChecking no
IdentityFile ~/.ssh/id_rsa-ec2
UserKnownHostsFile ~/.ssh/ec2_hosts
Always connect as user root to amazonaws.com boxes, do not ask for accepting the host’s key, and use the ec2 private key for authentication.
Update: It’s also useful to define a separate known hosts file, so your regular one does not get cluttered with host keys from AWS test systems.