I cannot figure out from documentation and source code how to define size of the root device.
You can specify N additional block devices using BlockDeviceMappings sectio
See Stackoverflow: How to launch EC2 instance with Boto, specifying size of EBS?
Also, here's a way to do it from the AWS Command-Line Interface (CLI):
aws ec2 run-instances --image-id ami-xxxxxxxx --instance-type m1.xlarge --block-device-mappings '{"DeviceName": "/dev/sda1","Ebs" : { "VolumeSize" : 50 }}'